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Merge branch 'ibm_float'

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This commit is contained in:
Robert Smallshire
2015-04-17 12:11:08 +02:00
parent 8f35206733 90574122d5
commit 5ab4c70969
57 changed files with 5301 additions and 2246 deletions
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.gitignore
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# Data
data/
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
@@ -53,7 +56,7 @@ coverage.xml
*.pot
# Sphinx documentation
docs/_build/
docs/build/
# Event stores
*.events
.travis.yml
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language: python
python:
- "2.7"
- "3.3"
- "3.4"
# command to install dependencies
install:
- "pip install -r test/test-requirements.txt"
# command to run tests
script: nosetests
DESCRIPTION.rst
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The SEG Y file format is one of several standards developed by the Society of Exploration Geophysicists for storing
geophysical seismic data. It is an open standard, and is controlled by the SEG Technical Standards Committee, a
non-profit organization.
This project aims to implement an open SEG Y module in Python for transporting seismic data between SEG Y files and
Python data structures in pure Python.
Status
======
*Segpy 2* is currently in alpha, so expect rough edges. That said, it seems to broadly work and is largely feature
complete.
What It Does
============
How To Get It
=============
*Segpy* is available on the Python Package index and can be installed with ``pip``::
$ pip install segpy
Requirements
============
*Segpy 2* work with Python 3.2 and higher (and 2.7 for now). For the majority of use *Segpy 2* has no external
dependencies. Optional modules with further dependencies such as *Numpy* are included in the ``segpy.ext`` package of
extras.
GUI/demogtk.py
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#!/usr/bin/env python
#Licence: GPLv2.0
#Copyright: Dave Aitel
import sys
try:
import pygtk
#tell pyGTK, if possible, that we want GTKv2
pygtk.require("2.0")
except:
print "You need to install pyGTK or GTKv2 or set your PYTHONPATH correctly"
print "try: export PYTHONPATH=/usr/local/lib/python2.2/site-packages/"
sys.exit(1)
import gtk
import gtk.glade
import segypy
#now we have both gtk and gtk.glade imported
#Also, we know we are running GTKv2
def insert_row(model,parent,firstcolumn,secondcolumn):
myiter=model.insert_after(parent,None)
model.set_value(myiter,0,firstcolumn)
model.set_value(myiter,1,secondcolumn)
return myiter
class appgui:
def __init__(self):
"""
In this init we are going to display the main serverinfo window
"""
gladefile="project1.glade"
windowname="serverinfo"
self.wTree=gtk.glade.XML (gladefile,windowname)
#we only have one callback to register, but you could register
#any number, or use a special class that
#automatically registers all callbacks
dic = { "on_button1_clicked" : self.button1_clicked,
"on_serverinfo_destroy" : (gtk.mainquit)}
self.wTree.signal_autoconnect (dic)
self.logwindowview=self.wTree.get_widget("textview1")
self.logwindow=gtk.TextBuffer(None)
self.logwindowview.set_buffer(self.logwindow)
import gobject
self.treeview=self.wTree.get_widget("treeview1")
self.treemodel=gtk.TreeStore(gobject.TYPE_STRING,
gobject.TYPE_INT,
gobject.TYPE_STRING)
self.treeview.set_model(self.treemodel)
self.treeview.set_headers_visible(True)
renderer=gtk.CellRendererText()
column=gtk.TreeViewColumn("Name",renderer, text=0)
column.set_resizable(True)
self.treeview.append_column(column)
renderer=gtk.CellRendererText()
column=gtk.TreeViewColumn("Description",renderer, text=1)
column.set_resizable(True)
self.treeview.append_column(column)
self.treeview.show()
model=self.treemodel
treeSTH=insert_row(model,None,'Segy Trace Header', '')
for key in segypy.TRACE_HEADER_DEF.keys():
insert_row(model,treeSTH,key, 'An Empty Row')
treeSH=insert_row(model,None,'Segy Header', 'SH')
for key in segypy.HEADER_DEF.keys():
insert_row(model,treeSH,key, 'An Empty Row')
return
#####CALLLBACKS
def button1_clicked(self,widget):
print "button clicked"
host=self.wTree.get_widget("entry1").get_text()
port=int(self.wTree.get_widget("spinbutton1").get_value())
if host=="":
return
import urllib
page=urllib.urlopen("http://"+host+":"+str(port)+"/")
data=page.read()
try:
#this changed in a revision of pyGTK2
self.logwindow.insert_at_cursor(data,len(data))
except:
self.logwindow.insert_at_cursor(data)
#print data
return
app=appgui()
gtk.main()
GUI/gui.py
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#!/usr/bin/python2.4
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#
# Small test to demonstrate glade.XML.signal_autoconnect on an instance
#
import pygtk
pygtk.require('2.0')
import matplotlib
matplotlib.use('GTK')
from matplotlib.figure import Figure
from matplotlib.axes import Subplot
from matplotlib.backends.backend_gtk import FigureCanvasGTK, NavigationToolbar
from matplotlib.numerix import arange, sin, pi
import Numeric as numpy
import gtk, gtk.glade
import segypy
def insert_row(model,parent,firstcolumn,secondcolumn,thirdcolumn):
myiter=model.insert_after(parent,None)
model.set_value(myiter,0,firstcolumn)
model.set_value(myiter,1,secondcolumn)
model.set_value(myiter,2,thirdcolumn)
# print secondcolumn
# return myiter
def update_segyplot(self):
self.figure = Figure(figsize=(6,4), dpi=72)
self.axis = self.figure.add_subplot(111)
self.axis.set_xlabel('Trace Header')
self.axis.set_ylabel('Time [s]')
self.axis.set_title(self.segy[1]['filename'])
self.axis.grid(True)
self.axis.imshow(self.segy[0])
self.canvas = FigureCanvasGTK(self.figure) # a gtk.DrawingArea
self.canvas.show()
self.graphview = self.xml.get_widget("vbox4")
self.graphview.pack_start(self.canvas, True, True)
def init_treeviews(self):
import gobject
###############################################################
# SEGYHEADER VIEW
self.treeview1 = self.xml.get_widget("treeview1")
self.treemodel1 = gtk.TreeStore(gobject.TYPE_STRING,
gobject.TYPE_STRING,
gobject.TYPE_STRING)
self.treeview1.set_model(self.treemodel1)
self.treeview1.set_headers_visible(True)
# COLUMN 1
renderer= gtk.CellRendererText()
self.tvcolumn1 = gtk.TreeViewColumn('Name', renderer, text=0)
self.tvcolumn1.set_resizable(True)
self.treeview1.append_column(self.tvcolumn1)
# COLUMN 2
renderer= gtk.CellRendererText()
self.tvcolumn2 = gtk.TreeViewColumn('Meaning', renderer, text=1)
self.tvcolumn2.set_resizable(True)
self.treeview1.append_column(self.tvcolumn2)
# COLUMN 3
renderer= gtk.CellRendererText()
self.tvcolumn3 = gtk.TreeViewColumn('Value', renderer, text=2)
self.tvcolumn3.set_resizable(True)
self.treeview1.append_column(self.tvcolumn3)
###############################################################
# SEGYHEADER VIEW
self.treeview2 = self.xml.get_widget("treeview2")
self.treemodel2 = gtk.TreeStore(gobject.TYPE_STRING,
gobject.TYPE_STRING,
gobject.TYPE_STRING)
self.treeview2.set_model(self.treemodel2)
self.treeview2.set_headers_visible(True)
# COLUMN 1
renderer= gtk.CellRendererText()
self.tvcolumn1 = gtk.TreeViewColumn('Name', renderer, text=0)
self.tvcolumn1.set_resizable(True)
self.treeview2.append_column(self.tvcolumn1)
# COLUMN 2
renderer= gtk.CellRendererText()
self.tvcolumn2 = gtk.TreeViewColumn('Meaning', renderer, text=1)
self.tvcolumn2.set_resizable(True)
self.treeview2.append_column(self.tvcolumn2)
# COLUMN 3
renderer= gtk.CellRendererText()
self.tvcolumn3 = gtk.TreeViewColumn('Value', renderer, text=2)
self.tvcolumn3.set_resizable(True)
self.treeview2.append_column(self.tvcolumn3)
def update_segyheader(self):
import gobject
# INSERT INTO TREEMODEL
self.SHtree= {"init": 1}
for key in segypy.HEADER_DEF.keys():
SHkey=segypy.HEADER_DEF[key]
if (SHkey.has_key('descr')):
descr = segypy.HEADER_DEF[key]['descr'][0][self.segy[1][key]]
else:
descr = ''
insert_row(self.treemodel1,None,key,descr,self.segy[1][key])
self.treeview1.show()
def update_segytraceheader(self,itrace=1):
import gobject
# INSERT INTO TREEMODEL
self.STHtree= {"init": 1}
for key in segypy.TRACE_HEADER_DEF.keys():
STHkey=segypy.TRACE_HEADER_DEF[key]
if (STHkey.has_key('descr')):
try:
descr = segypy.TRACE_HEADER_DEF[key]['descr'][0][self.segy[2][key][itrace-1]]
except:
descr='Not Defined'
else:
descr = ''
insert_row(self.treemodel2,None,key,descr,self.segy[2][key][itrace-1])
self.treeview2.show()
class SimpleTest:
def __init__(self):
self.xml = gtk.glade.XML('segygui/segygui.glade')
self.xml.signal_autoconnect(self)
init_treeviews(self)
self.window1 = self.xml.get_widget("window1")
self.window1.resize(600,400)
def on_cut1_activate(self, button):
self.hpaned1= self.xml.get_widget("hpaned1")
self.vbox3= self.xml.get_widget("vbox3")
pos = self.hpaned1.get_position()
if (pos==1):
pos=100
self.vbox3.visible = 1
else:
pos=1
self.vbox3.visible = 0
pos = self.hpaned1.set_position(pos)
print self.vbox3.visible
#width,height = self.vbox3.get_size()
#print width,height
# self.window1.resize(400,400)
def on_about1_activate(self, button):
dialog = gtk.AboutDialog()
dialog.set_name("SegyPY GUI")
dialog.set_version(segypy.version.__str__())
dialog.set_copyright("\302\251 Copyright 200x Thomas Mejer Hansen")
dialog.set_website("http://segymat.sourceforge.net/segypy/")
authors=["Thomas Mejer Hansen"]
dialog.set_authors(authors)
try:
f=open('LICENSE')
license = f.read(100000)
except IOError:
license = 'Could not read license file....';
dialog.set_license(license)
## Close dialog on user response
dialog.connect ("response", lambda d, r: d.destroy())
dialog.show()
def on_open1_activate(self, button):
dialog = gtk.FileChooserDialog("Open..",
None,
gtk.FILE_CHOOSER_ACTION_OPEN,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
gtk.STOCK_OPEN, gtk.RESPONSE_OK))
dialog.set_default_response(gtk.RESPONSE_OK)
filter = gtk.FileFilter()
filter.set_name("All files")
filter.add_pattern("*")
dialog.add_filter(filter)
filter = gtk.FileFilter()
filter.set_name("SEG-Y files")
filter.add_pattern("*.segy")
filter.add_pattern("*.sgy")
filter.add_pattern("*.seg-y")
dialog.add_filter(filter)
filter = gtk.FileFilter()
filter.set_name("SU files")
filter.add_pattern("*.su")
dialog.add_filter(filter)
response = dialog.run()
if response == gtk.RESPONSE_OK:
print dialog.get_filename(), 'selected'
filename = dialog.get_filename()
dialog.destroy()
self.segy = segypy.read_segy(filename)
update_segyheader(self)
update_segytraceheader(self)
update_segyplot(self)
def on_new1_activate(self, button):
self.segy = segypy.read_segy('../data_4byteINT.segy')
update_segyheader(self)
update_segytraceheader(self,1)
update_segyplot(self)
test = SimpleTest()
gtk.main()
GUI/project1.glade
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<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-interface SYSTEM "http://glade.gnome.org/glade-2.0.dtd">
<glade-interface>
<widget class="GtkWindow" id="serverinfo">
<property name="visible">True</property>
<property name="title" translatable="yes">Server Info</property>
<property name="type">GTK_WINDOW_TOPLEVEL</property>
<property name="window_position">GTK_WIN_POS_NONE</property>
<property name="modal">False</property>
<property name="resizable">True</property>
<property name="destroy_with_parent">False</property>
<property name="decorated">True</property>
<property name="skip_taskbar_hint">False</property>
<property name="skip_pager_hint">False</property>
<property name="type_hint">GDK_WINDOW_TYPE_HINT_NORMAL</property>
<property name="gravity">GDK_GRAVITY_NORTH_WEST</property>
<property name="focus_on_map">True</property>
<signal name="destroy" handler="on_serverinfo_destroy" last_modification_time="Wed, 15 Jan 2003 16:24:14 GMT"/>
<child>
<widget class="GtkVBox" id="vbox1">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkHBox" id="hbox1">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">8</property>
<child>
<widget class="GtkLabel" id="label1">
<property name="visible">True</property>
<property name="label" translatable="yes">Host:</property>
<property name="use_underline">False</property>
<property name="use_markup">False</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
<property name="ellipsize">PANGO_ELLIPSIZE_NONE</property>
<property name="width_chars">-1</property>
<property name="single_line_mode">False</property>
<property name="angle">0</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<widget class="GtkEntry" id="entry1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="editable">True</property>
<property name="visibility">True</property>
<property name="max_length">0</property>
<property name="text" translatable="yes"></property>
<property name="has_frame">True</property>
<property name="invisible_char">*</property>
<property name="activates_default">False</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
<child>
<widget class="GtkSpinButton" id="spinbutton1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="climb_rate">1</property>
<property name="digits">0</property>
<property name="numeric">False</property>
<property name="update_policy">GTK_UPDATE_ALWAYS</property>
<property name="snap_to_ticks">False</property>
<property name="wrap">False</property>
<property name="adjustment">80 1 65535 1 10 10</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<widget class="GtkButton" id="button1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="label" translatable="yes">GO!</property>
<property name="use_underline">True</property>
<property name="relief">GTK_RELIEF_NORMAL</property>
<property name="focus_on_click">True</property>
<signal name="clicked" handler="on_button1_clicked" last_modification_time="Wed, 15 Jan 2003 15:10:01 GMT"/>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<widget class="GtkScrolledWindow" id="scrolledwindow1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="hscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="vscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="shadow_type">GTK_SHADOW_NONE</property>
<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
<child>
<widget class="GtkTextView" id="textview1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="editable">True</property>
<property name="overwrite">False</property>
<property name="accepts_tab">True</property>
<property name="justification">GTK_JUSTIFY_LEFT</property>
<property name="wrap_mode">GTK_WRAP_NONE</property>
<property name="cursor_visible">True</property>
<property name="pixels_above_lines">0</property>
<property name="pixels_below_lines">0</property>
<property name="pixels_inside_wrap">0</property>
<property name="left_margin">0</property>
<property name="right_margin">0</property>
<property name="indent">0</property>
<property name="text" translatable="yes"></property>
</widget>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<widget class="GtkScrolledWindow" id="scrolledwindow2">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="hscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="vscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="shadow_type">GTK_SHADOW_NONE</property>
<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
<child>
<widget class="GtkTreeView" id="treeview1">
<property name="width_request">130</property>
<property name="height_request">226</property>
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="headers_visible">True</property>
<property name="rules_hint">False</property>
<property name="reorderable">False</property>
<property name="enable_search">True</property>
<property name="fixed_height_mode">False</property>
<property name="hover_selection">False</property>
<property name="hover_expand">False</property>
</widget>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
</child>
</widget>
</glade-interface>
GUI/segygui/segygui.glade
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<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-interface SYSTEM "http://glade.gnome.org/glade-2.0.dtd">
<glade-interface>
<widget class="GtkWindow" id="window1">
<property name="visible">True</property>
<property name="title" translatable="yes">Segy Viewer</property>
<property name="type">GTK_WINDOW_TOPLEVEL</property>
<property name="window_position">GTK_WIN_POS_CENTER</property>
<property name="modal">False</property>
<property name="resizable">True</property>
<property name="destroy_with_parent">False</property>
<property name="icon_name">stock_chart-reorganize</property>
<property name="decorated">True</property>
<property name="skip_taskbar_hint">False</property>
<property name="skip_pager_hint">False</property>
<property name="type_hint">GDK_WINDOW_TYPE_HINT_NORMAL</property>
<property name="gravity">GDK_GRAVITY_NORTH_WEST</property>
<property name="focus_on_map">True</property>
<property name="urgency_hint">False</property>
<child>
<widget class="GtkVBox" id="vbox1">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkMenuBar" id="menubar1">
<property name="visible">True</property>
<property name="pack_direction">GTK_PACK_DIRECTION_LTR</property>
<property name="child_pack_direction">GTK_PACK_DIRECTION_LTR</property>
<child>
<widget class="GtkMenuItem" id="menuitem1">
<property name="visible">True</property>
<property name="label" translatable="yes">_File</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem1_menu">
<child>
<widget class="GtkImageMenuItem" id="new1">
<property name="visible">True</property>
<property name="label">gtk-new</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_new1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="open1">
<property name="visible">True</property>
<property name="label">gtk-open</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_open1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save1">
<property name="visible">True</property>
<property name="label">gtk-save</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_save1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save_as1">
<property name="visible">True</property>
<property name="label">gtk-save-as</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_save_as1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkSeparatorMenuItem" id="separatormenuitem1">
<property name="visible">True</property>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="quit1">
<property name="visible">True</property>
<property name="label">gtk-quit</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_quit1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem2">
<property name="visible">True</property>
<property name="label" translatable="yes">_Edit</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem2_menu">
<child>
<widget class="GtkMenuItem" id="segy_header1">
<property name="visible">True</property>
<property name="label" translatable="yes">Segy Header</property>
<property name="use_underline">True</property>
<signal name="activate" handler="on_segy_header1_activate" last_modification_time="Mon, 10 Oct 2005 07:29:34 GMT"/>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="trace_header1">
<property name="visible">True</property>
<property name="label" translatable="yes">Trace Header</property>
<property name="use_underline">True</property>
<signal name="activate" handler="on_trace_header1_activate" last_modification_time="Mon, 10 Oct 2005 07:29:34 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="cut1">
<property name="visible">True</property>
<property name="label">gtk-cut</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_cut1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="copy1">
<property name="visible">True</property>
<property name="label">gtk-copy</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_copy1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="paste1">
<property name="visible">True</property>
<property name="label">gtk-paste</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_paste1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="delete1">
<property name="visible">True</property>
<property name="label">gtk-delete</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_delete1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem3">
<property name="visible">True</property>
<property name="label" translatable="yes">_View</property>
<property name="use_underline">True</property>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem4">
<property name="visible">True</property>
<property name="label" translatable="yes">_Help</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem4_menu">
<child>
<widget class="GtkMenuItem" id="about1">
<property name="visible">True</property>
<property name="label" translatable="yes">_About</property>
<property name="use_underline">True</property>
<signal name="activate" handler="on_about1_activate" last_modification_time="Sun, 09 Oct 2005 20:43:06 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<widget class="GtkHPaned" id="hpaned1">
<property name="width_request">385</property>
<property name="visible">True</property>
<property name="can_focus">True</property>
<child>
<widget class="GtkVBox" id="vbox3">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkNotebook" id="notebook1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="show_tabs">True</property>
<property name="show_border">True</property>
<property name="tab_pos">GTK_POS_TOP</property>
<property name="scrollable">False</property>
<property name="enable_popup">False</property>
<child>
<placeholder/>
</child>
<child>
<widget class="GtkLabel" id="label1">
<property name="visible">True</property>
<property name="label" translatable="yes">Plot</property>
<property name="use_underline">False</property>
<property name="use_markup">False</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
<property name="ellipsize">PANGO_ELLIPSIZE_NONE</property>
<property name="width_chars">-1</property>
<property name="single_line_mode">False</property>
<property name="angle">0</property>
</widget>
<packing>
<property name="type">tab</property>
</packing>
</child>
<child>
<widget class="GtkScrolledWindow" id="scrolledwindow1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="hscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="vscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="shadow_type">GTK_SHADOW_IN</property>
<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
<child>
<widget class="GtkTreeView" id="treeview1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="headers_visible">True</property>
<property name="rules_hint">False</property>
<property name="reorderable">False</property>
<property name="enable_search">True</property>
<property name="fixed_height_mode">False</property>
<property name="hover_selection">False</property>
<property name="hover_expand">False</property>
</widget>
</child>
</widget>
<packing>
<property name="tab_expand">False</property>
<property name="tab_fill">True</property>
</packing>
</child>
<child>
<widget class="GtkLabel" id="label3">
<property name="visible">True</property>
<property name="label" translatable="yes">Header</property>
<property name="use_underline">False</property>
<property name="use_markup">False</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
<property name="ellipsize">PANGO_ELLIPSIZE_NONE</property>
<property name="width_chars">-1</property>
<property name="single_line_mode">False</property>
<property name="angle">0</property>
</widget>
<packing>
<property name="type">tab</property>
</packing>
</child>
<child>
<widget class="GtkVBox" id="vbox5">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkHBox" id="hbox1">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<widget class="GtkArrow" id="arrow3">
<property name="width_request">15</property>
<property name="visible">True</property>
<property name="arrow_type">GTK_ARROW_LEFT</property>
<property name="shadow_type">GTK_SHADOW_OUT</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
<signal name="button_press_event" handler="on_arrow3_button_press_event" last_modification_time="Mon, 17 Oct 2005 10:28:17 GMT"/>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
<child>
<widget class="GtkHScale" id="hscale1">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="draw_value">False</property>
<property name="value_pos">GTK_POS_TOP</property>
<property name="digits">0</property>
<property name="update_policy">GTK_UPDATE_DISCONTINUOUS</property>
<property name="inverted">False</property>
<property name="adjustment">0 0 100 0 0 0</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
<child>
<widget class="GtkArrow" id="arrow2">
<property name="width_request">15</property>
<property name="visible">True</property>
<property name="arrow_type">GTK_ARROW_RIGHT</property>
<property name="shadow_type">GTK_SHADOW_OUT</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
<signal name="button_press_event" handler="on_arrow2_button_press_event" last_modification_time="Mon, 17 Oct 2005 10:28:03 GMT"/>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
<child>
<widget class="GtkScrolledWindow" id="scrolledwindow2">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="hscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="vscrollbar_policy">GTK_POLICY_ALWAYS</property>
<property name="shadow_type">GTK_SHADOW_IN</property>
<property name="window_placement">GTK_CORNER_TOP_LEFT</property>
<child>
<widget class="GtkTreeView" id="treeview2">
<property name="visible">True</property>
<property name="can_focus">True</property>
<property name="headers_visible">True</property>
<property name="rules_hint">False</property>
<property name="reorderable">False</property>
<property name="enable_search">True</property>
<property name="fixed_height_mode">False</property>
<property name="hover_selection">False</property>
<property name="hover_expand">False</property>
</widget>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
<packing>
<property name="tab_expand">False</property>
<property name="tab_fill">True</property>
</packing>
</child>
<child>
<widget class="GtkLabel" id="label4">
<property name="visible">True</property>
<property name="label" translatable="yes">Trace</property>
<property name="use_underline">False</property>
<property name="use_markup">False</property>
<property name="justify">GTK_JUSTIFY_LEFT</property>
<property name="wrap">False</property>
<property name="selectable">False</property>
<property name="xalign">0.5</property>
<property name="yalign">0.5</property>
<property name="xpad">0</property>
<property name="ypad">0</property>
<property name="ellipsize">PANGO_ELLIPSIZE_NONE</property>
<property name="width_chars">-1</property>
<property name="single_line_mode">False</property>
<property name="angle">0</property>
</widget>
<packing>
<property name="type">tab</property>
</packing>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
</widget>
<packing>
<property name="shrink">True</property>
<property name="resize">False</property>
</packing>
</child>
<child>
<widget class="GtkVBox" id="vbox4">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="shrink">True</property>
<property name="resize">True</property>
</packing>
</child>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">True</property>
<property name="fill">True</property>
</packing>
</child>
<child>
<widget class="GtkStatusbar" id="statusbar1">
<property name="visible">True</property>
<property name="has_resize_grip">True</property>
</widget>
<packing>
<property name="padding">0</property>
<property name="expand">False</property>
<property name="fill">False</property>
</packing>
</child>
</widget>
</child>
</widget>
</glade-interface>
GUI/test/test.glade
-251
View File
@@ -1,251 +0,0 @@
<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-interface SYSTEM "http://glade.gnome.org/glade-2.0.dtd">
<glade-interface>
<widget class="GtkWindow" id="window1">
<property name="width_request">800</property>
<property name="height_request">600</property>
<property name="visible">True</property>
<property name="title" translatable="yes">SegyPY GUI</property>
<property name="type">GTK_WINDOW_TOPLEVEL</property>
<property name="window_position">GTK_WIN_POS_NONE</property>
<property name="modal">False</property>
<property name="resizable">True</property>
<property name="destroy_with_parent">False</property>
<property name="decorated">True</property>
<property name="skip_taskbar_hint">False</property>
<property name="skip_pager_hint">False</property>
<property name="type_hint">GDK_WINDOW_TYPE_HINT_NORMAL</property>
<property name="gravity">GDK_GRAVITY_NORTH_WEST</property>
<property name="focus_on_map">True</property>
<property name="urgency_hint">False</property>
<child>
<widget class="GtkTable" id="table1">
<property name="width_request">307</property>
<property name="visible">True</property>
<property name="can_default">True</property>
<property name="has_default">True</property>
<property name="n_rows">3</property>
<property name="n_columns">1</property>
<property name="homogeneous">False</property>
<property name="row_spacing">0</property>
<property name="column_spacing">0</property>
<child>
<widget class="GtkMenuBar" id="menubar1">
<property name="visible">True</property>
<property name="pack_direction">GTK_PACK_DIRECTION_LTR</property>
<property name="child_pack_direction">GTK_PACK_DIRECTION_LTR</property>
<child>
<widget class="GtkMenuItem" id="menuitem1">
<property name="visible">True</property>
<property name="label" translatable="yes">_File</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem1_menu">
<child>
<widget class="GtkImageMenuItem" id="new1">
<property name="visible">True</property>
<property name="label">gtk-new</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_new1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="open1">
<property name="visible">True</property>
<property name="label">gtk-open</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_open1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save1">
<property name="visible">True</property>
<property name="label">gtk-save</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_save1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save_as1">
<property name="visible">True</property>
<property name="label">gtk-save-as</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_save_as1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkSeparatorMenuItem" id="separatormenuitem1">
<property name="visible">True</property>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="quit1">
<property name="visible">True</property>
<property name="label">gtk-quit</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_quit1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem2">
<property name="visible">True</property>
<property name="label" translatable="yes">_Edit</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem2_menu">
<child>
<widget class="GtkImageMenuItem" id="cut1">
<property name="visible">True</property>
<property name="label">gtk-cut</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_cut1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="copy1">
<property name="visible">True</property>
<property name="label">gtk-copy</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_copy1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="paste1">
<property name="visible">True</property>
<property name="label">gtk-paste</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_paste1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="delete1">
<property name="visible">True</property>
<property name="label">gtk-delete</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_delete1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem3">
<property name="visible">True</property>
<property name="label" translatable="yes">_View</property>
<property name="use_underline">True</property>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem4">
<property name="visible">True</property>
<property name="label" translatable="yes">_Help</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem4_menu">
<child>
<widget class="GtkMenuItem" id="about1">
<property name="visible">True</property>
<property name="label" translatable="yes">_About</property>
<property name="use_underline">True</property>
<signal name="activate" handler="on_about1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
</widget>
<packing>
<property name="left_attach">0</property>
<property name="right_attach">1</property>
<property name="top_attach">0</property>
<property name="bottom_attach">1</property>
<property name="x_options">fill</property>
<property name="y_options"></property>
</packing>
</child>
<child>
<widget class="GtkToolbar" id="toolbar1">
<property name="visible">True</property>
<property name="orientation">GTK_ORIENTATION_HORIZONTAL</property>
<property name="toolbar_style">GTK_TOOLBAR_BOTH</property>
<property name="tooltips">True</property>
<property name="show_arrow">True</property>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="left_attach">0</property>
<property name="right_attach">1</property>
<property name="top_attach">1</property>
<property name="bottom_attach">2</property>
<property name="x_options">fill</property>
<property name="y_options"></property>
</packing>
</child>
<child>
<widget class="GtkVBox" id="vbox1">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="left_attach">0</property>
<property name="right_attach">1</property>
<property name="top_attach">2</property>
<property name="bottom_attach">3</property>
<property name="x_options">fill</property>
</packing>
</child>
</widget>
</child>
</widget>
</glade-interface>
GUI/test/test.glade.bak
-250
View File
@@ -1,250 +0,0 @@
<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-interface SYSTEM "http://glade.gnome.org/glade-2.0.dtd">
<glade-interface>
<widget class="GtkWindow" id="window1">
<property name="width_request">800</property>
<property name="height_request">600</property>
<property name="visible">True</property>
<property name="title" translatable="yes">SegyPY GUI</property>
<property name="type">GTK_WINDOW_TOPLEVEL</property>
<property name="window_position">GTK_WIN_POS_NONE</property>
<property name="modal">False</property>
<property name="resizable">True</property>
<property name="destroy_with_parent">False</property>
<property name="decorated">True</property>
<property name="skip_taskbar_hint">False</property>
<property name="skip_pager_hint">False</property>
<property name="type_hint">GDK_WINDOW_TYPE_HINT_NORMAL</property>
<property name="gravity">GDK_GRAVITY_NORTH_WEST</property>
<property name="focus_on_map">True</property>
<property name="urgency_hint">False</property>
<child>
<widget class="GtkTable" id="table1">
<property name="visible">True</property>
<property name="can_default">True</property>
<property name="has_default">True</property>
<property name="n_rows">3</property>
<property name="n_columns">1</property>
<property name="homogeneous">False</property>
<property name="row_spacing">0</property>
<property name="column_spacing">0</property>
<child>
<widget class="GtkMenuBar" id="menubar1">
<property name="visible">True</property>
<property name="pack_direction">GTK_PACK_DIRECTION_LTR</property>
<property name="child_pack_direction">GTK_PACK_DIRECTION_LTR</property>
<child>
<widget class="GtkMenuItem" id="menuitem1">
<property name="visible">True</property>
<property name="label" translatable="yes">_File</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem1_menu">
<child>
<widget class="GtkImageMenuItem" id="new1">
<property name="visible">True</property>
<property name="label">gtk-new</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_new1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="open1">
<property name="visible">True</property>
<property name="label">gtk-open</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_open1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save1">
<property name="visible">True</property>
<property name="label">gtk-save</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_save1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="save_as1">
<property name="visible">True</property>
<property name="label">gtk-save-as</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_save_as1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkSeparatorMenuItem" id="separatormenuitem1">
<property name="visible">True</property>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="quit1">
<property name="visible">True</property>
<property name="label">gtk-quit</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_quit1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem2">
<property name="visible">True</property>
<property name="label" translatable="yes">_Edit</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem2_menu">
<child>
<widget class="GtkImageMenuItem" id="cut1">
<property name="visible">True</property>
<property name="label">gtk-cut</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_cut1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="copy1">
<property name="visible">True</property>
<property name="label">gtk-copy</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_copy1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="paste1">
<property name="visible">True</property>
<property name="label">gtk-paste</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_paste1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
<child>
<widget class="GtkImageMenuItem" id="delete1">
<property name="visible">True</property>
<property name="label">gtk-delete</property>
<property name="use_stock">True</property>
<signal name="activate" handler="on_delete1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem3">
<property name="visible">True</property>
<property name="label" translatable="yes">_View</property>
<property name="use_underline">True</property>
</widget>
</child>
<child>
<widget class="GtkMenuItem" id="menuitem4">
<property name="visible">True</property>
<property name="label" translatable="yes">_Help</property>
<property name="use_underline">True</property>
<child>
<widget class="GtkMenu" id="menuitem4_menu">
<child>
<widget class="GtkMenuItem" id="about1">
<property name="visible">True</property>
<property name="label" translatable="yes">_About</property>
<property name="use_underline">True</property>
<signal name="activate" handler="on_about1_activate" last_modification_time="Sat, 08 Oct 2005 11:26:31 GMT"/>
</widget>
</child>
</widget>
</child>
</widget>
</child>
</widget>
<packing>
<property name="left_attach">0</property>
<property name="right_attach">1</property>
<property name="top_attach">0</property>
<property name="bottom_attach">1</property>
<property name="x_options">fill</property>
<property name="y_options"></property>
</packing>
</child>
<child>
<widget class="GtkToolbar" id="toolbar1">
<property name="visible">True</property>
<property name="orientation">GTK_ORIENTATION_HORIZONTAL</property>
<property name="toolbar_style">GTK_TOOLBAR_BOTH</property>
<property name="tooltips">True</property>
<property name="show_arrow">True</property>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="left_attach">0</property>
<property name="right_attach">1</property>
<property name="top_attach">1</property>
<property name="bottom_attach">2</property>
<property name="x_options">fill</property>
<property name="y_options"></property>
</packing>
</child>
<child>
<widget class="GtkVBox" id="vbox1">
<property name="visible">True</property>
<property name="homogeneous">False</property>
<property name="spacing">0</property>
<child>
<placeholder/>
</child>
<child>
<placeholder/>
</child>
</widget>
<packing>
<property name="left_attach">0</property>
<property name="right_attach">1</property>
<property name="top_attach">2</property>
<property name="bottom_attach">3</property>
<property name="x_options">fill</property>
</packing>
</child>
</widget>
</child>
</widget>
</glade-interface>
GUI/test/test.gladep
-8
View File
@@ -1,8 +0,0 @@
<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-project SYSTEM "http://glade.gnome.org/glade-project-2.0.dtd">
<glade-project>
<name>Test</name>
<program_name>test</program_name>
<gnome_support>FALSE</gnome_support>
</glade-project>
GUI/test/test.gladep.bak
-8
View File
@@ -1,8 +0,0 @@
<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
<!DOCTYPE glade-project SYSTEM "http://glade.gnome.org/glade-project-2.0.dtd">
<glade-project>
<name>Test</name>
<program_name>test</program_name>
<gnome_support>FALSE</gnome_support>
</glade-project>
README.rst
+20 -26
View File
@@ -1,34 +1,28 @@
=====
Segpy
=====
=======
Segpy 2
=======
Status
======
Build status: rewrite branch:
.. image:: https://travis-ci.org/rob-smallshire/segpy.svg?branch=rewrite
:target: https://travis-ci.org/rob-smallshire/segpy
What is Segpy?
==============
The SEG Y file format is one of several standards developed by the Society of Exploration Geophysicists for storing
geophysical seismic data. It is an open standard, and is controlled by the SEG Technical Standards Committee, a
non-profit organization.
This project aims to implement an open SEG Y module in Python for transporting seismic data between SEG Y files and
Numpy arrays. Segpy is a package for reading, writing and manipulating SEG Y data in pure Python.
Python data structures in pure Python.
History
=======
Segpy Versions
==============
Segpy is a fork of a seemingly abandoned Python SEG Y reader called `SegyPY <http://segymat.sourceforge.net/segypy/>`_
which was last updated in 2005. I couldn't get a response from the original author of SegyPY and since it the code was
under an LGPL license I took the decision in 2011 to fork and run a new project on Google Code, under a the name of
*Segpy* avoid confusion. In July 2014 the project was again migrated from a now defunct Mercurial repository on Google
Code to this Git repository on GitHub.
The aim of the revived project is to fix serious problems with the code base in the area of correctness and
performance, but also to update it to work with contemporary Python environments including Python 2.7 and Python 3.
**Pull requests, bug reports and suggestions for improvements are most welcome!**
Authors
=======
* Robert Smallshire 2011 to date
* Thomas Mejer Hansen 2005
The Ibm2Ieee conversion routines are developed and made availabe for SegyPY by Secchi Angelo, who thanks Howard
Lightstone and Anton Vredegoor for their help.
Segpy 2.0 is a complete re-imagining of a SEG Y reader in Python and represents a complete break from Segpy 1.0 in terms
of the interface it presents to clients and the implementation behind those interfaces. Segpy 1.0 should be considered
unmaintained legacy software. The present and future of Segpy is Segpy 2.
docs/Makefile
+177
View File
@@ -0,0 +1,177 @@
# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = build
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
endif
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " xml to make Docutils-native XML files"
@echo " pseudoxml to make pseudoxml-XML files for display purposes"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
clean:
rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Segpy.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Segpy.qhc"
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/Segpy"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Segpy"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
latexpdfja:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through platex and dvipdfmx..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
docs/docs-requirements.txt
+2
View File
@@ -0,0 +1,2 @@
sphinx
sphinx_rtd_theme
docs/make.bat
+242
View File
@@ -0,0 +1,242 @@
@ECHO OFF
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set BUILDDIR=build
set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
set I18NSPHINXOPTS=%SPHINXOPTS% source
if NOT "%PAPER%" == "" (
set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
)
if "%1" == "" goto help
if "%1" == "help" (
:help
echo.Please use `make ^<target^>` where ^<target^> is one of
echo. html to make standalone HTML files
echo. dirhtml to make HTML files named index.html in directories
echo. singlehtml to make a single large HTML file
echo. pickle to make pickle files
echo. json to make JSON files
echo. htmlhelp to make HTML files and a HTML help project
echo. qthelp to make HTML files and a qthelp project
echo. devhelp to make HTML files and a Devhelp project
echo. epub to make an epub
echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
echo. text to make text files
echo. man to make manual pages
echo. texinfo to make Texinfo files
echo. gettext to make PO message catalogs
echo. changes to make an overview over all changed/added/deprecated items
echo. xml to make Docutils-native XML files
echo. pseudoxml to make pseudoxml-XML files for display purposes
echo. linkcheck to check all external links for integrity
echo. doctest to run all doctests embedded in the documentation if enabled
goto end
)
if "%1" == "clean" (
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
del /q /s %BUILDDIR%\*
goto end
)
%SPHINXBUILD% 2> nul
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
echo.installed, then set the SPHINXBUILD environment variable to point
echo.to the full path of the 'sphinx-build' executable. Alternatively you
echo.may add the Sphinx directory to PATH.
echo.
echo.If you don't have Sphinx installed, grab it from
echo.http://sphinx-doc.org/
exit /b 1
)
if "%1" == "html" (
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/html.
goto end
)
if "%1" == "dirhtml" (
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
goto end
)
if "%1" == "singlehtml" (
%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
goto end
)
if "%1" == "pickle" (
%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the pickle files.
goto end
)
if "%1" == "json" (
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the JSON files.
goto end
)
if "%1" == "htmlhelp" (
%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run HTML Help Workshop with the ^
.hhp project file in %BUILDDIR%/htmlhelp.
goto end
)
if "%1" == "qthelp" (
%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run "qcollectiongenerator" with the ^
.qhcp project file in %BUILDDIR%/qthelp, like this:
echo.^> qcollectiongenerator %BUILDDIR%\qthelp\Segpy.qhcp
echo.To view the help file:
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\Segpy.ghc
goto end
)
if "%1" == "devhelp" (
%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished.
goto end
)
if "%1" == "epub" (
%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The epub file is in %BUILDDIR%/epub.
goto end
)
if "%1" == "latex" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
if errorlevel 1 exit /b 1
echo.
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdf" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf
cd %BUILDDIR%/..
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdfja" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf-ja
cd %BUILDDIR%/..
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "text" (
%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The text files are in %BUILDDIR%/text.
goto end
)
if "%1" == "man" (
%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The manual pages are in %BUILDDIR%/man.
goto end
)
if "%1" == "texinfo" (
%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
goto end
)
if "%1" == "gettext" (
%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
goto end
)
if "%1" == "changes" (
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
if errorlevel 1 exit /b 1
echo.
echo.The overview file is in %BUILDDIR%/changes.
goto end
)
if "%1" == "linkcheck" (
%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
if errorlevel 1 exit /b 1
echo.
echo.Link check complete; look for any errors in the above output ^
or in %BUILDDIR%/linkcheck/output.txt.
goto end
)
if "%1" == "doctest" (
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
if errorlevel 1 exit /b 1
echo.
echo.Testing of doctests in the sources finished, look at the ^
results in %BUILDDIR%/doctest/output.txt.
goto end
)
if "%1" == "xml" (
%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The XML files are in %BUILDDIR%/xml.
goto end
)
if "%1" == "pseudoxml" (
%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
goto end
)
:end
docs/source/conf.py
+272
View File
@@ -0,0 +1,272 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Segpy documentation build configuration file, created by
# sphinx-quickstart on Sat Jan 31 17:56:17 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys
# on_rtd is whether we are on readthedocs.org
import os
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.todo',
'sphinx.ext.ifconfig',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = 'Segpy'
copyright = '2015, Robert Smallshire'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '2.0.0'
# The full version, including alpha/beta/rc tags.
release = '2.0.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = []
# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
if not on_rtd: # only import and set the theme if we're building docs locally
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# otherwise, readthedocs.org uses their theme by default, so no need to specify it
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'Segpydoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
('index', 'Segpy.tex', 'Segpy Documentation',
'Robert Smallshire', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'segpy', 'Segpy Documentation',
['Robert Smallshire'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'Segpy', 'Segpy Documentation',
'Robert Smallshire', 'Segpy', 'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
docs/source/index.rst
+49
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@@ -0,0 +1,49 @@
.. Segpy documentation master file, created by
sphinx-quickstart on Sat Jan 31 17:56:17 2015.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
=====
Segpy
=====
*Segpy* is a Python package for reading and writing SEG Y data. The SEG Y file format is one of several standards
developed by the Society of Exploration Geophysicists for storing geophysical seismic data. It is an open standard, and
is controlled by the SEG Technical Standards Committee, a non-profit organization.
This project aims to implement an open SEG Y module in Python for transporting seismic data between SEG Y files and
Python data structures.
Contents
========
Front Matter
------------
.. toctree::
:maxdepth: 2
Narrative Documentation
-----------------------
Read this to learn how to use *Segpy*:
Reference Documentation
-----------------------
Descriptions and examples for every public function, class and method in *Segpy*.
Change History
--------------
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
examples/loadsave.py
+52
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@@ -0,0 +1,52 @@
"""A simple example which loads a SEG Y file and saves it again.
Usage:
loadsave.py <in.segy> <out.segy>
"""
from __future__ import print_function
import os
import sys
import traceback
from segpy.reader import create_reader
from segpy.writer import write_segy
def load_save(in_filename, out_filename):
with open(in_filename, 'rb') as in_file, \
open(out_filename, 'wb') as out_file:
segy_reader = create_reader(in_file)
write_segy(out_file, segy_reader)
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
try:
in_filename = argv[0]
out_filename = argv[1]
except IndexError:
print(globals()['__doc__'], file=sys.stderr)
return os.EX_USAGE
try:
load_save(in_filename, out_filename)
except (FileNotFoundError, IsADirectoryError) as e:
print(e, file=sys.stderr)
return os.EX_NOINPUT
except PermissionError as e:
print(e, file=sys.stderr)
return os.EX_NOPERM
except Exception as e:
traceback.print_exception(type(e), e, e.__traceback__, file=sys.stderr)
return os.EX_SOFTWARE
return os.EX_OK
if __name__ == '__main__':
sys.exit(main())
examples/report.py
+81
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@@ -0,0 +1,81 @@
"""Displays a simple report of a SEG Y file.
Usage:
report.py <in.segy>
"""
from __future__ import print_function
import os
import sys
import traceback
from segpy.reader import create_reader
def report_segy(in_filename):
with open(in_filename, 'rb') as in_file:
segy_reader = create_reader(in_file)
print()
print("Filename: ", segy_reader.filename)
print("SEG Y revision: ", segy_reader.revision)
print("Number of traces: ", segy_reader.num_traces())
print("Data format: ",
segy_reader.data_sample_format_description)
print("Dimensionality: ", segy_reader.dimensionality)
try:
print("Number of CDPs: ", segy_reader.num_cdps())
except AttributeError:
pass
try:
print("Number of inlines: ", segy_reader.num_inlines())
print("Number of crosslines: ", segy_reader.num_xlines())
except AttributeError:
pass
print("=== BEGIN TEXTUAL REEL HEADER ===")
for line in segy_reader.textual_reel_header:
print(line[3:])
print("=== END TEXTUAL REEL HEADER ===")
print()
print("=== BEGIN EXTENDED TEXTUAL HEADER ===")
print(segy_reader.extended_textual_header)
print("=== END EXTENDED TEXTUAL_HEADER ===")
for trace_index in segy_reader.trace_indexes():
trace_header = segy_reader.trace_header(trace_index)
print("Inline {}, Crossline {}, Shotpoint {}".format(trace_header.Inline3D, trace_header.Crossline3D,
trace_header.ShotPoint))
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
try:
in_filename = argv[0]
except IndexError:
print(globals()['__doc__'], file=sys.stderr)
return os.EX_USAGE
try:
report_segy(in_filename)
except (FileNotFoundError, IsADirectoryError) as e:
print(e, file=sys.stderr)
return os.EX_NOINPUT
except PermissionError as e:
print(e, file=sys.stderr)
return os.EX_NOPERM
except Exception as e:
traceback.print_exception(type(e), e, e.__traceback__, file=sys.stderr)
return os.EX_SOFTWARE
return os.EX_OK
if __name__ == '__main__':
sys.exit(main())
examples/timed_reader.py
+68
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@@ -0,0 +1,68 @@
"""A simple example which times reading of all traces in a SEG Y file.
Usage:
timed_reader.py <in.segy>
"""
from __future__ import print_function
import datetime
import os
import sys
import traceback
from segpy.reader import create_reader
def read_traces(in_filename):
with open(in_filename, 'rb') as in_file:
t0 = datetime.datetime.now()
segy_reader = create_reader(in_file)
t1 = datetime.datetime.now()
for trace_index in segy_reader.trace_indexes():
trace = segy_reader.trace_samples(trace_index)
t2 = datetime.datetime.now()
time_to_read_header = (t1 - t0).total_seconds()
time_to_read_traces = (t2 - t1).total_seconds()
time_to_read_both = (t2 - t0).total_seconds()
print("Time to read headers : {} seconds", time_to_read_header)
print("Time to read traces : {} seconds", time_to_read_traces)
print("Total time : {} seconds", time_to_read_both)
def main(argv=None):
if argv is None:
argv = sys.argv[1:]
try:
in_filename = argv[0]
except IndexError:
print(globals()['__doc__'], file=sys.stderr)
return os.EX_USAGE
try:
read_traces(in_filename)
except (FileNotFoundError, IsADirectoryError) as e:
print(e, file=sys.stderr)
return os.EX_NOINPUT
except PermissionError as e:
print(e, file=sys.stderr)
return os.EX_NOPERM
except Exception as e:
traceback.print_exception(type(e), e, e.__traceback__, file=sys.stderr)
return os.EX_SOFTWARE
return os.EX_OK
if __name__ == '__main__':
sys.exit(main())
examples/timeslice.py
+137
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@@ -0,0 +1,137 @@
"""Extract a timeslice from a 3D seismic volume to a Numpy array.
Usage: timeslice.py [-h] [--dtype DTYPE] [--null NULL]
segy-file npy-file slice-index
Positional arguments:
segy-file Path to an existing SEG Y file of 3D seismic data
npy-file Path to the Numpy array file to be created for the timeslice
slice-index Zero based index of the time slice to be extracted
Optional arguments:
-h, --help show this help message and exit
--dtype DTYPE Numpy data type. If not provided a dtype compatible with the
SEG Y data will be used.
--null NULL Sample value to use for missing or short traces.
Example:
timeslice.py stack_final_int8.sgy slice_800.npy 800 --null=42.0 --dtype=f
"""
from __future__ import print_function
import argparse
import os
import sys
import traceback
import numpy as np
from segpy.reader import create_reader
from segpy_numpy.numpy.dtypes import make_dtype
class DimensionalityError(Exception):
pass
def extract_timeslice(segy_filename, out_filename, slice_index, dtype=None, null=0):
"""Extract a timeslice from a 3D SEG Y file to a Numpy NPY file.
Args:
segy_filename: Filename of a SEG Y file.
out_filename: Filename of the NPY file.
slice_index: The zero-based index (increasing with depth) of the slice to be extracted.
dtype: Optional Numpy dtype for the result array. If not provided a dtype compatible with
the SEG Y data will be used.
null: Optional sample value to use for missing or short traces. Defaults to zero.
"""
with open(segy_filename, 'rb') as segy_file:
segy_reader = create_reader(segy_file)
if dtype is None:
dtype = make_dtype(segy_reader.data_sample_format)
if segy_reader.dimensionality != 3:
raise DimensionalityError("Cannot slice {n} dimensional seismic.".format(segy_reader.dimensionality))
i_line_range = segy_reader.inline_range()
x_line_range = segy_reader.xline_range()
i_size = len(i_line_range)
x_size = len(x_line_range)
t_size = segy_reader.max_num_trace_samples()
if not (0 <= slice_index < t_size):
raise ValueError("Time slice index {0} out of range {} to {}".format(slice_index, 0, t_size))
timeslice = np.full((x_size, i_size), null, dtype)
for inline_num, xline_num in segy_reader.inline_xline_numbers():
trace_index = segy_reader.trace_index((inline_num, xline_num))
trace = segy_reader.trace_samples(trace_index)
try:
sample = trace[slice_index]
except IndexError:
sample = null
i_index = inline_num - i_line_range.start
x_index = xline_num - x_line_range.start
timeslice[x_index, i_index] = sample
np.save(out_filename, timeslice)
def nullable_dtype(s):
return None if s == "" else np.dtype(s)
def main(argv=None):
parser = argparse.ArgumentParser()
parser.add_argument("segy_file", metavar="segy-file",
help="Path to an existing SEG Y file of 3D seismic data")
parser.add_argument("npy_file", metavar="npy-file",
help="Path to the Numpy array file to be created for the timeslice")
parser.add_argument("slice_index", metavar="slice-index", type=int,
help="Zero based index of the time slice to be extracted", )
parser.add_argument("--dtype", type=nullable_dtype, default="",
help="Numpy data type. If not provided a dtype compatible with the SEG Y data will be used.")
parser.add_argument("--null", type=float, default=0.0,
help="Sample value to use for missing or short traces.")
if argv is None:
argv = sys.argv[1:]
args = parser.parse_args(argv)
try:
extract_timeslice(args.segy_file,
args.npy_file,
args.slice_index,
args.dtype,
args.null)
except (FileNotFoundError, IsADirectoryError) as e:
print(e, file=sys.stderr)
return os.EX_NOINPUT
except PermissionError as e:
print(e, file=sys.stderr)
return os.EX_NOPERM
except Exception as e:
traceback.print_exception(type(e), e, e.__traceback__, file=sys.stderr)
return os.EX_SOFTWARE
return os.EX_OK
if __name__ == '__main__':
sys.exit(main())
ibm_float.py
-22
View File
@@ -1,22 +0,0 @@
import struct
def ibm2ieee2(ibm_float):
"""
ibm2ieee2(ibm_float)
Used by permission
(C) Secchi Angelo
with thanks to Howard Lightstone and Anton Vredegoor.
"""
dividend = float(16 ** 6)
if ibm_float == 0:
return 0.0
istic, a, b, c = struct.unpack('>BBBB', ibm_float)
if istic >= 128:
sign = -1.0
istic -= 128
else:
sign = 1.0
mant = float(a << 16) + float(b << 8) + float(c)
return sign * 16 ** (istic - 64) * (mant / dividend)
makerelease.sh
-15
View File
@@ -1,15 +0,0 @@
#!/bin/sh
VERSION=0.3
DIR=segypy-$VERSION
mkdir $DIR
cp segypy.py $DIR/.
cp testsegy.py $DIR/.
cp LICENSE $DIR/.
cp README $DIR/.
zip -r $DIR.zip $DIR
tar cvfz $DIR.tgz $DIR
rm -fr $DIR
plotting.py
-34
View File
@@ -1,34 +0,0 @@
def image_segy(Data):
"""
imageSegy(Data)
Image segy Data
"""
import pylab
pylab.imshow(Data)
pylab.title('pymat test')
pylab.grid(True)
pylab.show()
def wiggle(Data, SH, skipt=1, maxval=8, lwidth=0.1):
"""
wiggle(Data, SH)
"""
import pylab
t = range(SH['ns'])
for i in range(0, SH['ntraces'], skipt):
trace = Data[:, i]
trace[0] = 0
trace[SH['ns'] - 1] = 0
pylab.plot(i + trace / maxval, t, color='black', linewidth=lwidth)
for a in range(len(trace)):
if trace[a] < 0:
trace[a] = 0
pylab.fill(i + Data[:, i] / maxval, t, 'k', linewidth=0)
pylab.title(SH['filename'])
pylab.grid(True)
pylab.show()
segpy-ext/segpy-numpy/DESCRIPTION.rst
+20
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@@ -0,0 +1,20 @@
Segpy-Numpy offers tools for working with both *Segpy* and *Numpy*. See the *Segpy* documentation for further details.
What It Does
============
How To Get It
=============
*Segpy-Numpy* is available on the Python Package index and can be installed with ``pip``::
$ pip install segpy-numpy
Requirements
============
*Segpy-Numpy* should work with Python 3.2 and higher (and 2.7 for now). For the majority of use *Segpy 2* has no
externaldependencies. Optional modules with further dependencies such as *Numpy* are included in the ``segpy.ext``
package of extras.
segpy-ext/segpy-numpy/__init__.py
+1
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@@ -0,0 +1 @@
segpy-ext/segpy-numpy/segpy_numpy/__init__.py
+10
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@@ -0,0 +1,10 @@
print("segpy_numpy.__init__ imported")
from pkgutil import extend_path
#__path__ = extend_path(__path__, __name__)
__version__ = '2.0.0a1'
def load():
pass
segpy-ext/segpy-numpy/segpy_numpy/numpy/__init__.py
+1
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@@ -0,0 +1 @@
segpy-ext/segpy-numpy/segpy_numpy/numpy/dtypes.py
+32
View File
@@ -0,0 +1,32 @@
"""Optional interoperability with Numpy."""
import numpy
NUMPY_DTYPES = {'ibm': numpy.dtype('f4'),
'int32': numpy.dtype('i4'),
'int16': numpy.dtype('i2'),
'float32': numpy.dtype('f4'),
'int8': numpy.dtype('i1')}
def make_dtype(data_sample_format):
"""Convert a SEG Y data sample format to a compatible numpy dtype.
Note :
IBM float data sample formats ('ibm') will correspond to IEEE float data types.
Args:
data_sample_format: A data sample format string.
Returns:
A numpy.dtype instance.
Raises:
ValueError: For unrecognised data sample format strings.
"""
try:
return NUMPY_DTYPES[data_sample_format]
except KeyError:
raise ValueError("Unknown data sample format string {!r}".format(data_sample_format))
segpy-ext/segpy-numpy/setup.cfg
+5
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@@ -0,0 +1,5 @@
[bdist_wheel]
# This flag says that the code is written to work on both Python 2 and Python
# 3. If at all possible, it is good practice to do this. If you cannot, you
# will need to generate wheels for each Python version that you support.
universal=1
segpy-ext/segpy-numpy/setup.py
+127
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@@ -0,0 +1,127 @@
import io
import os
import re
from setuptools import setup, find_packages # Always prefer setuptools over distutils
from codecs import open # To use a consistent encoding
from os import path
def read(*names, **kwargs):
with io.open(
os.path.join(os.path.dirname(__file__), *names),
encoding=kwargs.get("encoding", "utf8")
) as fp:
return fp.read()
def find_version(*file_paths):
version_file = read(*file_paths)
version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
version_file, re.M)
if version_match:
return version_match.group(1)
raise RuntimeError("Unable to find version string.")
here = path.abspath(path.dirname(__file__))
def local_file(name):
return os.path.join(here, name)
# Get the long description from the relevant file
with open(local_file('DESCRIPTION.rst'), encoding='utf-8') as f:
long_description = f.read()
setup(
name='segpy-numpy',
# Versions should comply with PEP440. For a discussion on single-sourcing
# the version across setup.py and the project code, see
# https://packaging.python.org/en/latest/single_source_version.html
version=find_version("segpy_numpy/__init__.py"),
description='Interoperability between Numpy with Segpy.',
long_description=long_description,
# The project's main homepage.
url='https://github.com/rob-smallshire/segpy',
# Author details
author='Robert Smallshire',
author_email='robert@smallshire.org.uk',
# Choose your license
license='GPL',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 3 - Alpha',
# Indicate who your project is intended for
'Intended Audience :: Developers',
'Topic :: Scientific/Engineering',
'Topic :: Software Development :: Libraries',
# Pick your license as you wish (should match "license" above)
'License :: OSI Approved :: MIT License',
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
],
# What does your project relate to?
keywords='seismic geocomputing geophysics numpy',
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
packages=find_packages(here, exclude=['segpy', 'contrib', 'docs', 'test*']),
# List run-time dependencies here. These will be installed by pip when your
# project is installed. For an analysis of "install_requires" vs pip's
# requirements files see:
# https://packaging.python.org/en/latest/requirements.html
install_requires=['numpy'],
# List additional groups of dependencies here (e.g. development dependencies).
# You can install these using the following syntax, for example:
# $ pip install -e .[dev,test]
extras_require = {
'dev': ['check-manifest', 'wheel'],
'doc': ['sphinx', 'cartouche'],
'test': ['coverage', 'hypothesis'],
},
# If there are data files included in your packages that need to be
# installed, specify them here. If using Python 2.6 or less, then these
# have to be included in MANIFEST.in as well.
package_data={
},
# Although 'package_data' is the preferred approach, in some case you may
# need to place data files outside of your packages.
# see http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files
# In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
data_files=[],
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
# Declare entry-points to modules.
entry_points={
'segpy.ext': 'segpy-numpy = segpy_numpy'
},
)
segpy/__init__.py
+1
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@@ -0,0 +1 @@
__version__ = '2.0.0a1'
header_definition.py → segpy/binary_reel_header_definition.py
+2 -2
View File
@@ -2,7 +2,7 @@
SEG Y Header Definition
"""
from revisions import SEGY_REVISION_0, SEGY_REVISION_1
from segpy.revisions import SEGY_REVISION_0, SEGY_REVISION_1
HEADER_DEF = {"Job": {"pos": 3200, "type": "int32", "def": 0}}
HEADER_DEF["Line"] = {"pos": 3204, "type": "int32", "def": 0}
@@ -47,13 +47,13 @@ HEADER_DEF["DataSampleFormat"]["datatype"][SEGY_REVISION_1] = {
1: 'ibm',
2: 'l',
3: 'h',
# 5: 'float',
5: 'f',
8: 'B'}
HEADER_DEF["EnsembleFold"] = {"pos": 3226, "type": "int16", "def": 0}
HEADER_DEF["TraceSorting"] = {"pos": 3228, "type": "int16", "def": 0}
HEADER_DEF["VerticalSumCode"] = {"pos": 3230, "type": "int16", "def": 0}
HEADER_DEF["SweepFrequencyStart"] = {"pos": 3232, "type": "int16", "def": 0}
HEADER_DEF["SweepFrequencyEnd"] = {"pos": 3234, "type": "int16", "def": 0}
HEADER_DEF["SweepLength"] = {"pos": 3236, "type": "int16", "def": 0}
HEADER_DEF["SweepType"] = {"pos": 3238, "type": "int16", "def": 0}
segpy/caching.py
+48
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@@ -0,0 +1,48 @@
def lfu_cache(maxsize=100):
'''Least-frequently-used cache decorator.
Arguments to the cached function must be hashable.
Cache performance statistics stored in f.hits and f.misses.
Clear the cache with f.clear().
http://en.wikipedia.org/wiki/Least_Frequently_Used
'''
def decorating_function(user_function):
cache = {} # mapping of args to results
use_count = Counter() # times each key has been accessed
kwd_mark = object() # separate positional and keyword args
@functools.wraps(user_function)
def wrapper(*args, **kwds):
key = args
if kwds:
key += (kwd_mark,) + tuple(sorted(kwds.items()))
use_count[key] += 1
# get cache entry or compute if not found
try:
result = cache[key]
wrapper.hits += 1
except KeyError:
result = user_function(*args, **kwds)
cache[key] = result
wrapper.misses += 1
# purge least frequently used cache entry
if len(cache) > maxsize:
for key, _ in nsmallest(maxsize // 10,
use_count.iteritems(),
key=itemgetter(1)):
del cache[key], use_count[key]
return result
def clear():
cache.clear()
use_count.clear()
wrapper.hits = wrapper.misses = 0
wrapper.hits = wrapper.misses = 0
wrapper.clear = clear
return wrapper
return decorating_function
segpy/catalog.py
+588
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@@ -0,0 +1,588 @@
from abc import abstractmethod, ABCMeta
from collections import Mapping, Sequence, OrderedDict
from fractions import Fraction
from segpy.portability import reprlib
from segpy.util import contains_duplicates, measure_stride, minmax
class CatalogBuilder(object):
"""Use a catalog builder to construct optimised, immutable mappings.
A CatalogBuilder is useful when, depending on the particular keys and
values used, a more compact or efficient representation of the mapping
is possible than, say, a regular dictionary. The CatalogBuilder
accumulates values and then, once all values have been added, analyzes
the keys and values to produce a more optimized representation of the
mapping.
"""
def __init__(self, mapping=None):
"""Initialize a Catalog Builder.
Args:
mapping: An optional mapping (such as a dictionary) of items.
"""
self._catalog = []
if mapping is not None:
for key, value in mapping.items():
self.add(key, value)
def add(self, index, value):
"""Add an item.
Each index must be unique if create() is to be subsequently
called successfully, although duplicate index values will be
accepted by this call without complaint.
"""
self._catalog.append((index, value))
def create(self):
"""Create a possibly more optimized representation of the mapping.
In this worst case, this method returns an object which is
essentially an immutable dictionary. In the best case, the
space savings can be vast.
Returns:
A mapping, if a unique mapping from indexes to values is
possible, otherwise None.
"""
# This method examines the contents of the mapping using
# various heuristics to come up with a better representation.
if len(self._catalog) < 2:
return DictionaryCatalog(self._catalog)
# In-place sort by index
self._catalog.sort(key=lambda index_value: index_value[0])
if contains_duplicates(index for index, value in self._catalog):
return None
if all(isinstance(index, Sequence) and (len(index) == 2)
for index, value in self._catalog):
return self._create_catalog_2()
return self._create_catalog_1()
def _create_catalog_1(self):
"""Create a catalog for one-dimensional integer keys (i.e. scalars)
"""
index_min = self._catalog[0][0]
index_max = self._catalog[-1][0]
index_stride = measure_stride(index for index, value in self._catalog)
if index_stride is None:
# Dictionary strategy - arbitrary keys and values
return DictionaryCatalog(self._catalog)
self._catalog.sort(key=lambda index_value: index_value[1])
value_min = self._catalog[0][1]
value_max = self._catalog[-1][1]
value_stride = measure_stride(value for index, value in self._catalog)
if index_stride is not None and value_stride == 0:
assert value_min == value_max
return RegularConstantCatalog(index_min,
index_max,
index_stride,
value_min)
if index_stride is None and value_stride == 0:
assert value_min == value_max
return ConstantCatalog(
(index for index, value in self._catalog),
value_min)
if index_stride is not None and value_stride is None:
# Regular index - regular keys and arbitrary values
return RegularCatalog(index_min,
index_max,
index_stride,
(value for index, value in self._catalog))
assert (index_stride is not None) and (value_stride is not None)
catalog = LinearRegularCatalog(index_min,
index_max,
index_stride,
value_min,
value_max,
value_stride)
return catalog
def _create_catalog_2(self):
"""Create a catalog for two-dimensional integer keys.
Each key must be a two-element sequence.
"""
i_min, i_max = minmax(i for (i, j), value in self._catalog)
j_min, j_max = minmax(j for (i, j), value in self._catalog)
is_rm, diff = self._is_row_major(i_min, j_min, j_max)
if is_rm:
return RowMajorCatalog(i_min, i_max, j_min, j_max, diff)
return DictionaryCatalog(self._catalog)
def _is_row_major(self, i_min, j_min, j_max):
"""Does row major ordering predict values from keys?
In row-major order the last dimension is contiguous, and so changes
quickest, when moving through the elements in storage order. Hence
the number of rows is the number of distinct i values and the numbers
of elements in each row (i.e. columns) is the number of distinct j.
Args:
i_min: The minimum i value.
j_min: The minimum j value.
j_max: The maximum j value.
Returns:
A 2-tuple containing, in the first element True if the values can
be predicted from the keys by assuming a row-major ordering,
otherwise False. If True, the second element will be a constant
offset, otherwise it can be ignored.
"""
diff = None
for (i, j), actual_value in self._catalog:
proposed_value = (i - i_min) * (j_max + 1 - j_min) + (j - j_min)
current_diff = actual_value - proposed_value
if diff is None:
diff = current_diff
if current_diff != diff:
return False, None
return True, diff
class Catalog(Mapping):
"""An abstract base class for Catalogs which provides min and max keys and values."""
__metaclass__ = ABCMeta
@abstractmethod
def __init__(self, key_min=None, key_max=None, value_min=None, value_max=None):
"""Must be overridden and called by subclasses.
Args:
key_min: Optional minimum key.
key_max: Optional maximum key.
value_min: Optional minimum value.
value_max: Optional maximum value.
"""
self._min_key = key_min
self._max_key = key_max
self._min_value = value_min
self._max_value = value_max
def key_min(self):
"""Minimum key"""
if self._min_key is None:
self._min_key = min(self.keys())
return self._min_key
def key_max(self):
"""Maximum key"""
if self._max_key is None:
self._max_key = max(self.keys())
return self._max_key
def value_min(self):
"""Minimum value"""
if self._min_value is None:
self._min_value = min(self.values())
return self._min_value
def value_max(self):
"""Maximum value"""
if self._max_value is None:
self._max_value = max(self.values())
return self._max_value
class RowMajorCatalog(Catalog):
"""A mapping which assumes a row-major ordering of a two-dimensional matrix.
This is the ordering of items in a two-dimensional matrix where in
the (i, j) key tuple the j value changes fastest when iterating
through the items in order.
A RowMajorCatalog predicts the value v from the key (i, j) according to the
following formula:
v = (i - i_min) * j_max + (j - j_min) + c
for
i_min <= i <= i_max
j_min <= j <= j_max
and where c is an integer constant to allow zero- or one-based indexing.
"""
def __init__(self, i_min, i_max, j_min, j_max, c):
"""Initialize a RowMajorCatalog.
Args:
i_min (int): The minimum i value.
i_max (int): The maximum i value.
j_min (int): The minimum j value.
j_max (int): The maximum j value.
c (int): The constant offset
"""
super(RowMajorCatalog, self).__init__()
self._i_min = i_min
self._i_max = i_max
self._j_min = j_min
self._j_max = j_max
self._c = c
@property
def i_min(self):
"""Minimum i value"""
return self._i_min
@property
def i_max(self):
"""Maximum i value"""
return self._i_max
@property
def j_min(self):
"""Minimum j value"""
return self._j_min
@property
def j_max(self):
"""Maximum j value"""
return self._j_max
def key_min(self):
"""Minimum (i, j) key"""
return self._i_min, self._j_min
def key_max(self):
"""Maximum (i, j) key"""
return self._i_max, self._j_max
def value_min(self):
"""Minimum value at key_min"""
return self[self.key_min()]
def value_max(self):
"""Maximum value at key_max"""
return self[self.key_max()]
def __getitem__(self, key):
i, j = key
if not (self._i_min <= i <= self._i_max) and \
(self._j_min <= j <= self._j_max):
raise KeyError("{!r} key {!r} out of range".format(self, key))
value = (i - self._i_min) * (self._j_max + 1 - self._j_min) + (j - self._j_min) + self._c
return value
def __contains__(self, key):
i, j = key
return (self._i_min <= i <= self._i_max) and \
(self._j_min <= j <= self._j_max)
def __len__(self):
return (self._i_max - self._i_min) * (self._j_max + 1 - self._j_min)
def __iter__(self):
for i in range(self._i_min, self._i_max + 1):
for j in range(self._j_min, self._j_max + 1):
yield (i, j)
def __repr__(self):
return '{}({}, {}, {}, {}, {})'.format(
self.__class__.__name__,
self._i_min, self._i_max, self._j_min, self._j_max, self._c)
class DictionaryCatalog(Catalog):
"""An immutable, ordered, dictionary mapping.
"""
def __init__(self, items):
super(DictionaryCatalog, self).__init__()
self._items = OrderedDict(items)
def __getitem__(self, key):
return self._items[key]
def __iter__(self):
return iter(self._items)
def __len__(self):
return len(self._items)
def __contains__(self, item):
return item in self._items
def __repr__(self):
return '{}({})'.format(
self.__class__.__name__, reprlib.repr(self._items.items()))
class RegularConstantCatalog(Catalog):
"""Mapping with keys ordered with regular spacing along the number line.
The values associated with the keys are constant.
"""
def __init__(self, key_min, key_max, key_stride, value):
"""Initialize a RegularConstantCatalog.
The catalog is initialized by a description of how the keys
are distributed along the number line, and a value which
corresponds with all keys.
Args:
key_min: The minimum key.
key_max: The maximum key.
key_stride: The difference between successive keys.
value: A value associated with all keys.
"""
key_range = key_max - key_min
if key_range % key_stride != 0:
raise ValueError("RegularIndex key range {!r} is not "
"a multiple of stride {!r}".format(
key_stride, key_range))
super(RegularConstantCatalog, self).__init__(
key_min=key_min,
key_max=key_max,
value_min=value,
value_max=value)
self._key_stride = key_stride
def __getitem__(self, key):
if key not in self:
raise KeyError("{!r} does not contain key {!r}".format(self, key))
return self.value_min()
def __len__(self):
return 1 + (self.key_max() - self.key_min()) / self._key_stride
def __contains__(self, key):
return (self.key_min() <= key <= self.key_max()) and \
((key - self.key_min()) % self._key_stride == 0)
def __iter__(self):
return iter(range(self.key_min(),
self.key_max() + 1,
self._key_stride))
def __repr__(self):
return '{}({}, {}, {}, {})'.format(
self.__class__.__name__,
self.key_min(),
self.key_max(),
self._key_stride,
self.value_min())
class ConstantCatalog(Catalog):
"""Mapping with arbitrary keys and a single constant value.
"""
def __init__(self, keys, value):
"""Initialize a RegularConstantCatalog.
The catalog is initialized by a description with an iterable series of
keys and a constant value to be associated with all the keys.
Args:
keys: An iterable series of distinct keys.
key_max: The maximum key.
key_stride: The difference between successive keys.
value: A value associated with all keys.
"""
super(ConstantCatalog, self).__init__(value_min=value, value_max=value)
self._items = frozenset(keys)
def __getitem__(self, key):
if key not in self:
raise KeyError("{!r} does not contain key {!r}".format(self, key))
return self.value_min()
def __len__(self):
return len(self._items)
def __contains__(self, key):
return key in self._items
def __iter__(self):
return iter(self._items)
def __repr__(self):
return '{}({}, {})'.format(
self.__class__.__name__,
reprlib.repr(self._items),
self.value_min())
class RegularCatalog(Catalog):
"""Mapping with keys ordered with regular spacing along the number line.
The values associated with the keys are arbitrary.
"""
def __init__(self, key_min, key_max, key_stride, values):
"""Initialize a RegularCatalog.
The catalog is initialized by a description of how the keys
are distributed along the number line, and an iterable series of
corresponding values.
Args:
key_min: The minimum key.
key_max: The maximum key.
key_stride: The difference between successive keys.
values: An iterable series of values corresponding to the keys.
Raises:
ValueError: There is any inconsistency in the keys, stride,
and/or values.
"""
key_range = key_max - key_min
if key_range % key_stride != 0:
raise ValueError("{} key range {!r} is not "
"a multiple of stride {!r}".format(self.__class__.__name__,
key_stride, key_range))
super(RegularCatalog, self).__init__(key_min=key_min, key_max=key_max)
self._key_stride = key_stride
self._values = list(values)
num_keys = key_range // key_stride
if num_keys != len(self._values):
raise ValueError("{} key range and values inconsistent".format(self.__class__.__name__))
def __getitem__(self, key):
if not (self.key_min() <= key <= self.key_max()):
raise KeyError("{!r} key {!r} out of range".format(self, key))
offset = key - self.key_min()
if offset % self._key_stride != 0:
raise KeyError("{!r} does not contain key {!r}".format(self, key))
index = offset // self._key_stride
return self._values[index]
def __len__(self):
return len(self._values)
def __contains__(self, key):
return (self.key_min() <= key <= self.key_max()) and \
((key - self.key_min()) % self._key_stride == 0)
def __iter__(self):
return iter(range(self.key_min(),
self.key_max() + 1,
self._key_stride))
def __repr__(self):
return '{}({}, {}, {}, {})'.format(
self.__class__.__name__,
self.key_min(),
self.key_max(),
self._key_stride,
reprlib.repr(self._values))
class LinearRegularCatalog(Catalog):
"""A mapping which assumes a linear relationship between keys and values.
This is the ordering of items in a two-dimensional matrix where in
the (i, j) key tuple the j value changes fastest when iterating
through the items in order.
A LinearRegularCatalog predicts the value v from the key according to the
following formula:
v = (value_max - value_min) / (key_max - key_min) * (key - key_min) + value_min
"""
def __init__(self,
key_min,
key_max,
key_stride,
value_min,
value_max,
value_stride):
"""Initialize a LinearRegularCatalog.
Args:
key_min: The minimum key.
key_max: The maximum key.
key_stride: The difference between successive keys.
value_min: The minimum value.
value_max: The maximum value.
Raises:
ValueError: There is any inconsistency in the keys, strides,
and/or values.
"""
key_range = key_max - key_min
if key_range % key_stride != 0:
raise ValueError("{} key range {!r} is not "
"a multiple of key stride {!r}".format(
self.__class__.__name__,
key_stride,
key_range))
self._key_stride = key_stride
value_range = value_max - value_min
if value_range % value_stride != 0:
raise ValueError("{} value range {!r} is not "
"a multiple of value stride {!r}".format(
self.__class__.__name__,
value_stride,
value_range))
self._value_stride = value_stride
super(LinearRegularCatalog, self).__init__(
key_min=key_min,
key_max=key_max,
value_min=value_min,
value_max=value_max)
num_keys = (self.key_max() - self.key_min()) // self._key_stride
num_values = (self.value_max() - self.value_min()) // self._value_stride
if num_keys != num_values:
raise ValueError("{} inconsistent number of "
"keys {} and values {}".format(
self.__class__.__name__,
num_keys,
num_values))
self._m = Fraction(self.value_max() - self.value_min(),
self.key_max() - self.key_min())
def __getitem__(self, key):
if not (self.key_min() <= key <= self.key_max()):
raise KeyError("{!r} key {!r} out of range".format(self, key))
offset = key - self.key_min()
if offset % self._key_stride != 0:
raise KeyError("{!r} does not contain key {!r}".format(self, key))
v = self._m * (key - self.key_min()) + self.value_min()
assert v.denominator == 1
return v.numerator
def __len__(self):
return 1 + (self.key_max() - self.key_min()) // self._key_stride
def __contains__(self, key):
return (self.key_min() <= key <= self.key_max()) and \
((key - self.key_min()) % self._key_stride == 0)
def __iter__(self):
return iter(range(self.key_min(), self.key_max() + 1, self._key_stride))
def __repr__(self):
return '{}({}, {}, {}, {}, {}, {})'.format(
self.__class__.__name__,
self.key_min(),
self.key_max(),
self._key_stride,
self.value_min(),
self.value_max(),
self._value_stride)
segpy/datatypes.py
+39
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@@ -0,0 +1,39 @@
DATA_SAMPLE_FORMAT = {1: 'ibm',
2: 'int32',
3: 'int16',
5: 'float32',
8: 'int8'}
# A mapping from SEG Y data types to format characters used by the struct module
CTYPES = {'int32': 'i',
'uint32': 'I',
'int16': 'h',
'uint16': 'H',
'int8': 'b',
'uint8': 'B',
'float32': 'f',
'ibm': 'ibm'}
CTYPE_DESCRIPTION = {'ibm': 'IBM float',
'int32': '32 bit signed integer',
'uint32': '32 bit unsigned integer',
'int16': '16 bit signed integer',
'uint16': '16 bit unsigned integer',
'float32': 'IEEE float32',
'int8': '8 bit signed integer (byte)',
'uint8': '8 bit unsigned integer (byte)'}
SIZES = dict(i=4,
I=4,
h=2,
H=2,
b=1,
B=1,
f=4,
ibm=4)
def size_in_bytes(ctype):
return SIZES[ctype]
segpy/encoding.py
+78
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@@ -0,0 +1,78 @@
ASCII = 'ascii'
EBCDIC = 'cp037'
SUPPORTED_ENCODINGS = (ASCII, EBCDIC)
class UnsupportedEncodingError(Exception):
def __init__(self, text, encoding):
self._encoding = encoding
super(UnsupportedEncodingError, self).__init__(text)
@property
def encoding(self):
return self._encoding
def __str__(self):
return "{} not supported for encoding {}".format(self.args[0], self._encoding)
def __repr__(self):
return "{}({!r}, {!r}".format(self.__class__.__name__, self.args[0], self._encoding)
def is_supported_encoding(encoding):
return encoding in SUPPORTED_ENCODINGS
COMMON_CHARS = 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789:_- '
COMMON_EBCDIC_CHARS = set(COMMON_CHARS.encode(EBCDIC))
COMMON_ASCII_CHARS = set(COMMON_CHARS.encode(ASCII))
def guess_encoding(bs, threshold=0.5):
"""Try to determine whether the encoding of byte stream b is an ASCII string or an EBCDIC string.
Args:
bs: A byte string (Python 2 - str; Python 3 - bytes)
Returns:
A string which can be used with the Python encoding functions: 'cp037' for EBCDIC, 'ascii' for ASCII or None
if neither.
"""
ebcdic_count = 0
ascii_count = 0
null_count = 0
count = 0
for b in bs:
if b in COMMON_EBCDIC_CHARS:
ebcdic_count +=1
if b in COMMON_ASCII_CHARS:
ascii_count +=1
if b == 0:
null_count += 1
count += 1
if count == 0:
return None
ebcdic_freq = ebcdic_count / count
ascii_freq = ascii_count / count
null_freq = null_count / count
if null_freq == 1.0:
return ASCII # Doesn't matter
if ebcdic_freq < threshold and ascii_freq >= threshold:
return ASCII
if ebcdic_freq >= threshold and ascii_freq < threshold:
return EBCDIC
if ebcdic_freq < threshold and ascii_freq < threshold:
return None
return None
segpy/ext/__init__.py
+20
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@@ -0,0 +1,20 @@
import pkg_resources
loaded = set()
def load_entry_points(name=None):
"""Load extension packages into the segpy.ext namespace.
Any packages registered against the 'segpy.ext' entry-point group will be
installed dynamically into the segpy.ext namespace.
"""
for entry_point in pkg_resources.iter_entry_points(group='segpy.ext', name=name):
package = entry_point.load()
if package not in loaded:
loaded.add(package)
__path__.extend(package.__path__)
package.load()
load_entry_points()
segpy/ibm_float.py
+491
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@@ -0,0 +1,491 @@
from math import frexp, isnan, isinf, ceil, floor, trunc
from numbers import Real
from segpy.portability import long_int, byte_string, four_bytes
IBM_ZERO_BYTES = b'\x00\x00\x00\x00'
IBM_NEGATIVE_ONE_BYTES = b'\xc1\x10\x00\x00'
IBM_POSITIVE_ONE_BYTES = b'A\x10\x00\x00'
MIN_IBM_FLOAT = -7.2370051459731155e+75
LARGEST_NEGATIVE_NORMAL_IBM_FLOAT = -5.397605346934028e-79
SMALLEST_POSITIVE_NORMAL_IBM_FLOAT = 5.397605346934028e-79
MAX_IBM_FLOAT = 7.2370051459731155e+75
MAX_BITS_PRECISION_IBM_FLOAT = 24
MIN_BITS_PRECISION_IBM_FLOAT = 21 # The first 3 bits of the mantissa may be zero
EPSILON_IBM_FLOAT = pow(2.0, -(MIN_BITS_PRECISION_IBM_FLOAT - 1))
_L24 = long_int(2) ** MAX_BITS_PRECISION_IBM_FLOAT
_F24 = float(pow(2, MAX_BITS_PRECISION_IBM_FLOAT))
_L21 = long_int(2) ** MIN_BITS_PRECISION_IBM_FLOAT
EXPONENT_BIAS = 64
MIN_EXACT_INTEGER_IBM_FLOAT = -2**MAX_BITS_PRECISION_IBM_FLOAT
MAX_EXACT_INTEGER_IBM_FLOAT = 2**MIN_BITS_PRECISION_IBM_FLOAT
def ibm2ieee(big_endian_bytes):
"""Interpret a byte string as a big-endian IBM float.
Args:
big_endian_bytes (str): A string containing at least four bytes.
Returns:
The floating point value.
"""
a, b, c, d = four_bytes(big_endian_bytes)
if a == b == c == d == 0:
return 0.0
sign = -1 if (a & 0x80) else 1
exponent_16_biased = a & 0x7f
mantissa = ((b << 16) | (c << 8) | d) / _F24
value = sign * mantissa * pow(16, exponent_16_biased - EXPONENT_BIAS)
return value
BITS_PER_NYBBLE = 4
def truncate(big_endian_bytes):
a, b, c, d = four_bytes(big_endian_bytes)
sign = -1 if (a & 0x80) else 1
exponent_16_biased = a & 0x7f
exponent_16 = exponent_16_biased - EXPONENT_BIAS
mantissa = ((b << 16) | (c << 8) | d)
print("sign =", sign)
print("exponent_16", exponent_16, hex(exponent_16), bin(exponent_16))
print("mantissa", mantissa, hex(mantissa), bin(mantissa))
num_nybbles_to_preserve = min(exponent_16, MAX_BITS_PRECISION_IBM_FLOAT // BITS_PER_NYBBLE)
num_bits_to_clear = MAX_BITS_PRECISION_IBM_FLOAT - num_nybbles_to_preserve * BITS_PER_NYBBLE
clear_mask = 2**num_bits_to_clear - 1
preserve_mask = (2**MAX_BITS_PRECISION_IBM_FLOAT - 1) & ~clear_mask
print("num_nybbles_to_preserve", num_nybbles_to_preserve)
print("num_bits_to_clear", num_bits_to_clear)
print("clear_mask ", bin(clear_mask))
print("preserve_mask", bin(preserve_mask))
truncated_mantissa = mantissa & preserve_mask
value = truncated_mantissa * pow(16, exponent_16)
scaled_value = value >> MAX_BITS_PRECISION_IBM_FLOAT
return scaled_value
#
# tb = (preserve_mask >> 16) & b
# tc = (preserve_mask >> 8) & c
# td = preserve_mask & d
#
# return byte_string((a, tb, tc, td))
def ieee2ibm(f):
"""Convert a float to four big-endian bytes representing an IBM float.
Args:
f (float): The value to be converted.
Returns:
A bytes object (Python 3) or a string (Python 2) containing four
bytes representing a big-endian IBM float.
Raises:
OverflowError: If f is outside the representable range.
ValueError: If f is NaN or infinite.
FloatingPointError: If f cannot be represented without total loss of precision.
"""
if f == 0:
# There are many potential representations of zero - this is the standard one
return b'\x00\x00\x00\x00'
if isnan(f):
raise ValueError("NaN cannot be represented in IBM floating point")
if isinf(f):
raise ValueError("Infinities cannot be represented in IBM floating point")
if f < MIN_IBM_FLOAT:
raise OverflowError("IEEE Floating point value {} is less than the "
"representable minimum for IBM floats.".format(f))
if f > MAX_IBM_FLOAT:
raise OverflowError("IEEE Floating point value {} is greater than the "
"representable maximum for IBM floats".format(f))
# Now compute m and e to satisfy:
#
# f = m * 2^e
#
# where 0.5 <= abs(m) < 1
# except when f == 0 in which case m == 0 and e == 0, which we've already
# dealt with.
m, e = frexp(f)
# Convert the fraction (m) into an integer representation. IEEE float32
# numbers have 23 explicit (24 implicit) bits of precision.
mantissa = abs(long_int(m * _L24))
exponent = e
sign = 0x80 if f < 0 else 0x00
# IBM single precision floats are of the form
# (-1)^sign * 0.significand * 16^(exponent-64)
# Adjust the exponent, and the mantissa in sympathy so it is
# a multiple of four, so it can be expressed in base 16
remainder = exponent % 4
if remainder != 0:
shift = 4 - remainder
mantissa >>= shift
exponent += shift
exponent_16 = exponent >> 2 # Divide by four to convert to base 16
exponent_16_biased = exponent_16 + 64 # Add the exponent bias of 64
# If the biased exponent is negative, we try to use a subnormal representation
if exponent_16_biased < 0:
shift_16 = 0 - exponent_16_biased
exponent_16_biased += shift_16 # An increment of the base-16 exponent must be balanced by
mantissa >>= 4 * shift_16 # A division by 16 (four binary places) in the mantissa
if mantissa == 0:
raise FloatingPointError("IEEE Floating point value {} is smaller than the "
"smallest subnormal number for IBM floats.".format(f))
a = sign | exponent_16_biased
b = (mantissa >> 16) & 0xff
c = (mantissa >> 8) & 0xff
d = mantissa & 0xff
return byte_string((a, b, c, d))
class IBMFloat(Real):
__slots__ = ['_data']
_INTERNED = {IBM_ZERO_BYTES: None,
IBM_NEGATIVE_ONE_BYTES: None,
IBM_POSITIVE_ONE_BYTES: None}
# noinspection PyUnresolvedReferences
def __new__(cls, b):
obj = object.__new__(cls)
data = bytes(b)
num_bytes = len(data)
if num_bytes != 4:
raise ValueError("{} cannot be constructed from {} values".format(cls.__name__, num_bytes))
obj._data = data
# Intern common values
if data in cls._INTERNED:
if cls._INTERNED[data] is None:
cls._INTERNED[data] = obj
return cls._INTERNED[data]
return obj
@classmethod
def from_float(cls, f):
"""Construct an IBMFloat from an IEEE float.
Args:
f (float): The value to be converted.
Returns:
An IBMFloat.
Raises:
OverflowError: If f is outside the representable range.
ValueError: If f is NaN or infinite.
FloatingPointError: If f cannot be represented without total loss of precision.
"""
return cls(ieee2ibm(f))
@classmethod
def from_real(cls, f):
if isinstance(f, IBMFloat):
return f
return cls.from_float(f)
@classmethod
def from_bytes(cls, b):
return cls(b)
@classmethod
def ldexp(cls, fraction, exponent):
"""Make an IBMFloat from fraction and exponent.
The is the inverse function of IBMFloat.frexp()
Args:
fraction: A Real in the range -1.0 to 1.0.
exponent: An integer in the range -256 to 255 inclusive.
"""
if not (-1.0 <= fraction <= 1.0):
raise ValueError("ldexp fraction {!r} out of range -1.0 to +1.0")
if not (-256 <= exponent < 256):
raise ValueError("ldexp exponent {!r} out of range -256 to 256")
ieee = fraction * 2**exponent
return IBMFloat.from_float(ieee)
@property
def signbit(self):
"""True if the value is negative, otherwise False."""
return bool(self._data[0] & 0x80)
def __float__(self):
return ibm2ieee(self._data)
def __bytes__(self):
return self._data
def __repr__(self):
return "{}.from_float({!r}) ~{!r}".format(self.__class__.__name__, self._data, float(self))
def __str__(self):
return str(float(self))
def __bool__(self):
return not self.is_zero()
def is_zero(self):
return self.int_mantissa == 0
def __nonzero__(self):
return not self.is_zero()
def is_subnormal(self):
if self.is_zero():
# Only one of the many possible representations of zero is considered 'normal' - all the zeros
return not all(b == 0 for b in self._data)
return self._data[1] < 16 # TODO: Replace magic number with constant
def zero_subnormal(self):
return IBM_FLOAT_ZERO if self.is_subnormal() else self
def frexp(self):
"""Obtain the fraction and exponent.
Returns:
A pair where the first item is the fraction in the range -1.0 and +1.0 and the
exponent is an integer such that f = fraction * 2**exponent
"""
sign = -1 if self.signbit else 1
mantissa = sign * self.int_mantissa / _F24
exp_2 = self.exp16 * 4
return mantissa, exp_2
def __pos__(self):
return self
def __neg__(self):
if self.is_zero():
return IBM_FLOAT_ZERO
data = self._data
return IBMFloat((data[0] ^ 0b10000000,
data[1],
data[2],
data[3]))
def __abs__(self):
if self.is_zero():
return IBM_FLOAT_ZERO
data = self._data
return IBMFloat((data[0] & 0b01111111,
data[1],
data[2],
data[3]))
def __eq__(self, rhs):
lhs = self
if not isinstance(rhs, IBMFloat):
return float(lhs) == float(rhs)
lhs_sign = lhs.signbit
rhs_sign = rhs.signbit
if lhs_sign != rhs_sign:
return False
nlhs = lhs.normalize()
nrhs = rhs.normalize()
if not (nlhs.is_subnormal() or nrhs.is_subnormal()):
# Both of the numbers are normalised
return nlhs._data == nrhs._data
# Either or both of the numbers are subnormal
lhs_exp16 = nlhs.exp16
rhs_exp16 = nrhs.exp16
lhs_mantissa = nlhs.int_mantissa
rhs_mantissa = nrhs.int_mantissa
if lhs_exp16 < rhs_exp16:
delta_exp16 = rhs_exp16 - lhs_exp16
lhs_mantissa >>= 4 * delta_exp16
lhs_exp16 += delta_exp16
if lhs_exp16 > rhs_exp16:
delta_exp16 = lhs_exp16 - rhs_exp16
rhs_mantissa >>= 4 * delta_exp16
rhs_exp16 += delta_exp16
assert lhs_exp16 == rhs_exp16
return lhs_mantissa == rhs_mantissa
def __floordiv__(self, rhs):
return float(self) // float(rhs)
def __rfloordiv__(self, lhs):
return float(lhs) // float(self)
def __rtruediv__(self, lhs):
q = float(lhs) / float(self)
return IBMFloat.from_float(q) if isinstance(lhs, float) else q
def __pow__(self, exponent):
p = pow(float(self), float(exponent))
return IBMFloat.from_float(p) if isinstance(exponent, IBMFloat) else p
def __rpow__(self, base):
return IBMFloat.from_float(pow(float(base), float(self)))
def __mod__(self, rhs):
m = float(self) % float(rhs)
return IBMFloat.from_float(m) if isinstance(rhs, IBMFloat) else m
def __rmod__(self, lhs):
m = float(lhs) % float(self)
return IBMFloat.from_float(m) if isinstance(lhs, IBMFloat) else m
def __rmul__(self, lhs):
p = float(lhs) * float(self)
return IBMFloat.from_float(p) if isinstance(lhs, IBMFloat) else p
def __radd__(self, lhs):
s = float(lhs) + float(self)
return IBMFloat.from_float(s) if isinstance(lhs, IBMFloat) else s
def __lt__(self, rhs):
return float(self) < float(rhs)
def __le__(self, rhs):
return float(self) <= float(rhs)
def __gt__(self, rhs):
return float(self) > float(rhs)
def __ge__(self, rhs):
return float(self) >= float(rhs)
def __ceil__(self):
t = trunc(self)
return t if self.signbit else t + 1
def __floor__(self):
t = trunc(self)
return t - 1 if self.signbit else t
@property
def exp16(self):
"""The base 16 exponent."""
exponent_16_biased = self._data[0] & 0x7f
exponent_16 = exponent_16_biased - EXPONENT_BIAS
return exponent_16
@property
def int_mantissa(self):
data = self._data
return (data[1] << 16) | (data[2] << 8) | data[3]
def __trunc__(self):
sign = -1 if self.signbit else 1
exponent_16 = self.exp16
mantissa = self.int_mantissa
num_nybbles_to_preserve = min(exponent_16, MAX_BITS_PRECISION_IBM_FLOAT // BITS_PER_NYBBLE)
num_bits_to_clear = MAX_BITS_PRECISION_IBM_FLOAT - num_nybbles_to_preserve * BITS_PER_NYBBLE
clear_mask = 2**num_bits_to_clear - 1
preserve_mask = (2**MAX_BITS_PRECISION_IBM_FLOAT - 1) & ~clear_mask
truncated_mantissa = mantissa & preserve_mask
magnitude = truncated_mantissa * pow(16, exponent_16) >> MAX_BITS_PRECISION_IBM_FLOAT
return sign * magnitude
def normalize(self):
"""Normalize the floating point value.
Returns:
A normalized IBMFloat equal in value to this object.
Raises:
FloatingPointError: If the number could not be normalized.
"""
if self.is_zero():
return IBM_FLOAT_ZERO
exponent_16 = self.exp16
mantissa = self.int_mantissa
while mantissa < (1 << 20):
new_exponent_16 = exponent_16 - 1
if not (-64 <= new_exponent_16 < 64):
raise FloatingPointError("Could not normalize {!r} without causing exponent overflow.".format(self))
mantissa <<= 4
exponent_16 = new_exponent_16
exponent_16_biased = exponent_16 + EXPONENT_BIAS
sign = int(self.signbit) << 7
a = sign | exponent_16_biased
b = (mantissa >> 16) & 0xff
c = (mantissa >> 8) & 0xff
d = mantissa & 0xff
return IBMFloat.from_bytes((a, b, c, d))
def __round__(self, ndigits=None):
return IBMFloat.from_float(round(float(self), ndigits))
def __truediv__(self, rhs):
q = float(self) / float(rhs)
return IBMFloat.from_float(q) if isinstance(rhs, IBMFloat) else q
def __mul__(self, rhs):
p = float(self) * float(rhs)
return IBMFloat.from_float(p) if isinstance(rhs, IBMFloat) else p
def __add__(self, rhs):
p = float(self) + float(rhs)
return IBMFloat.from_float(p) if isinstance(rhs, IBMFloat) else p
def __int__(self):
return trunc(self)
IBM_FLOAT_ZERO = IBMFloat.from_bytes(IBM_ZERO_BYTES)
segpy/portability.py
+78
View File
@@ -0,0 +1,78 @@
import os
import sys
EMPTY_BYTE_STRING = b'' if sys.version_info >= (3, 0) else ''
def seekable(fh):
"""Determine whether a file-like object supports seeking.
Args:
fh: The file-like-object to be tested.
Returns:
True if the file supports seeking, otherwise False.
"""
try:
return fh.seekable()
except AttributeError:
try:
pos = fh.tell()
try:
fh.seek(0, os.SEEK_END)
finally:
fh.seek(pos)
except AttributeError:
return False
return True
if sys.version_info >= (3, 0):
long_int = int
else:
long_int = long
if sys.version_info >= (3, 0):
def byte_string(integers):
return bytes(integers)
else:
def byte_string(integers):
return EMPTY_BYTE_STRING.join(chr(i) for i in integers)
if sys.version_info >= (3, 0):
import reprlib
reprlib = reprlib # Keep the static analyzer happy
else:
import repr as reprlib
if sys.version_info >= (3, 0):
izip = zip
from itertools import zip_longest as izip_longest
else:
from itertools import (izip, izip_longest)
izip = izip # Keep the static analyzer happy
izip_longest = izip_longest # Keep the static analyzer happy
if sys.version_info >= (3, 0):
def four_bytes(byte_str):
a, b, c, d = byte_str[:4]
return a, b, c, d
else:
def four_bytes(byte_str):
a = ord(byte_str[0])
b = ord(byte_str[1])
c = ord(byte_str[2])
d = ord(byte_str[3])
return a, b, c, d
if sys.version_info >= (3, 0):
unicode = str
else:
unicode = unicode
segpy/reader.py
+661
View File
@@ -0,0 +1,661 @@
from __future__ import print_function
from segpy.encoding import ASCII
from segpy.portability import seekable
from segpy.util import file_length, filename_from_handle
from segpy.datatypes import DATA_SAMPLE_FORMAT, CTYPE_DESCRIPTION, CTYPES, size_in_bytes
from segpy.toolkit import (extract_revision,
bytes_per_sample,
read_binary_reel_header,
read_trace_header,
catalog_traces,
read_binary_values,
compile_trace_header_format,
REEL_HEADER_NUM_BYTES,
TRACE_HEADER_NUM_BYTES,
read_textual_reel_header,
read_extended_textual_headers,
guess_textual_header_encoding)
def create_reader(fh, encoding=None, endian='>', progress=None):
"""Create a SegYReader (or one of its subclasses) based on performing
a scan of SEG Y data.
This function is the preferred method for creating SegYReader
objects. It reads basic header information and attempts to build
indexes for traces, CDP numbers (for 2D surveys), and inline and
cross line co-ordinates (for 3D surveys) to facilitate subsequent
random-access to traces.
Args:
fh: A file-like-object open in binary mode positioned such
that the beginning of the reel header will be the next
byte to be read. For disk-based SEG Y files, this is the
beginning of the file.
encoding: An optional text encoding for the textual headers. If
None (the default) a heuristic will be used to guess the
header encoding.
endian: '>' for big-endian data (the standard and default), '<'
for little-endian (non-standard)
progress: A unary callable which will be passed a number
between zero and one indicating the progress made. If
provided, this callback will be invoked at least once with
an argument equal to one.
Raises:
ValueError: ``fh`` is unsuitable for some reason, such as not
being open, not being seekable, not being in
binary mode, or being too short.
Returns:
A SegYReader object. Depending on the exact type of the
SegYReader returned different capabilities may be
available. Inspect the returned object to determine these
capabilities, or be prepared for capabilities not defined in
the SegYReader base class to be unavailable. The underlying
file-like object must remain open for the duration of use of
the returned reader object. It is the caller's responsibility
to close the underlying file.
Example:
with open('my_seismic_data.sgy', 'rb') as fh:
reader = create_reader(fh)
print(reader.num_traces())
"""
if hasattr(fh, 'encoding') and fh.encoding is not None:
raise TypeError(
"SegYReader must be provided with a binary mode file object")
if not seekable(fh):
raise TypeError(
"SegYReader must be provided with a seekable file object")
if fh.closed:
raise ValueError(
"SegYReader must be provided with an open file object")
num_file_bytes = file_length(fh)
if num_file_bytes < REEL_HEADER_NUM_BYTES:
raise ValueError(
"SEG Y file {!r} of {} bytes is too short".format(
filename_from_handle(fh),
num_file_bytes))
if endian not in ('<', '>'):
raise ValueError("Unrecognised endian value {!r}".format(endian))
if encoding is None:
encoding = guess_textual_header_encoding(fh)
if encoding is None:
encoding = ASCII
textual_reel_header = read_textual_reel_header(fh, encoding)
binary_reel_header = read_binary_reel_header(fh, endian)
extended_textual_header = read_extended_textual_headers(fh, binary_reel_header, encoding)
revision = extract_revision(binary_reel_header)
bps = bytes_per_sample(binary_reel_header, revision)
trace_offset_catalog, trace_length_catalog, cdp_catalog, line_catalog = catalog_traces(fh, bps, endian, progress)
if cdp_catalog is not None and line_catalog is None:
return SegYReader2D(fh, textual_reel_header, binary_reel_header, extended_textual_header, trace_offset_catalog,
trace_length_catalog, cdp_catalog, encoding, endian)
if cdp_catalog is None and line_catalog is not None:
return SegYReader3D(fh, textual_reel_header, binary_reel_header, extended_textual_header, trace_offset_catalog,
trace_length_catalog, line_catalog, encoding, endian)
return SegYReader(fh, textual_reel_header, binary_reel_header, extended_textual_header, trace_offset_catalog,
trace_length_catalog, encoding, endian)
class SegYReader(object):
"""A basic SEG Y reader.
Use to obtain read the reel header, the trace_samples headers or trace_samples
values. Traces can be accessed only by trace_samples index.
"""
def __init__(self,
fh,
textual_reel_header,
binary_reel_header,
extended_textual_headers,
trace_offset_catalog,
trace_length_catalog,
encoding,
endian='>'):
"""Initialize a SegYReader around a file-like-object.
Note:
Usually a SegYReader is most easily constructed using the
create_reader() function.
Args:
fh: A file-like object, which must support seeking and
support binary reading.
textual_reel_header: A sequence of forty 80-character Unicode strings
containing header data.
binary_reel_header: A dictionary containing reel header data.
extended_textual_headers: A sequence of sequences of Unicode strings.
trace_offset_catalog: A mapping from zero-based trace_samples index to
the byte-offset to individual traces within the file.
trace_length_catalog: A mapping from zero-based trace_samples index to the
number of samples in that trace_samples.
encoding: Either ASCII or EBCDIC.
endian: '>' for big-endian data (the standard and default), '<' for
little-endian (non-standard)
"""
self._fh = fh
self._endian = endian
self._encoding = encoding
self._trace_header_format = compile_trace_header_format(self._endian)
self._textual_reel_header = textual_reel_header
self._binary_reel_header = binary_reel_header
self._extended_textual_headers = extended_textual_headers
self._trace_offset_catalog = trace_offset_catalog
self._trace_length_catalog = trace_length_catalog
self._revision = extract_revision(self._binary_reel_header)
self._bytes_per_sample = bytes_per_sample(
self._binary_reel_header, self.revision)
def trace_indexes(self):
"""An iterator over zero-based trace_samples indexes.
Returns:
An iterator which yields integers in the range zero to
num_traces() - 1
"""
return iter(self._trace_offset_catalog)
def num_traces(self):
"""The number of traces"""
return len(self._trace_offset_catalog)
def max_num_trace_samples(self):
"""The number of samples in the trace_samples with the most samples."""
return self._trace_length_catalog.value_max()
def num_trace_samples(self, trace_index):
"""The number of samples in the specified trace_samples."""
return self._trace_length_catalog[trace_index]
def trace_samples(self, trace_index, start=None, stop=None):
"""Read a specific trace_samples.
Args:
trace_index: An integer in the range zero to num_traces() - 1
start: Optional zero-based start sample index. The default
is to read from the first (i.e. zeroth) sample.
stop: Optional zero-based stop sample index. Following Python
slice convention this is one beyond the end.
Returns:
A sequence of numeric trace_samples samples.
Example:
first_trace_samples = segy_reader.trace_samples(0)
part_of_second_trace_samples = segy_reader.trace_samples(1, 1000, 2000)
"""
if not (0 <= trace_index < self.num_traces()):
raise ValueError("Trace index out of range.")
num_samples_in_trace = self.num_trace_samples(trace_index)
start_sample = start if start is not None else 0
stop_sample = stop if stop is not None else num_samples_in_trace
if not (0 <= stop_sample <= num_samples_in_trace):
raise ValueError("trace_samples(): stop value {} out of range 0 to {}"
.format(stop, num_samples_in_trace))
if not (0 <= start_sample <= stop_sample):
raise ValueError("trace_samples(): start value {} out of range 0 to {}"
.format(start, stop_sample))
dsf = self._binary_reel_header['DataSampleFormat']
ctype = DATA_SAMPLE_FORMAT[dsf]
start_pos = (self._trace_offset_catalog[trace_index]
+ TRACE_HEADER_NUM_BYTES
+ start_sample * size_in_bytes(CTYPES[ctype]))
num_samples_to_read = stop_sample - start_sample
trace_values = read_binary_values(
self._fh, start_pos, ctype, num_samples_to_read, self._endian)
return trace_values
def trace_header(self, trace_index):
"""Read a specific trace_samples.
Args:
trace_index: An integer in the range zero to num_traces() - 1
Returns:
A TraceHeader corresponding to the requested trace_samples.
Example:
first_trace_header, first_trace_samples = segy_reader.trace_samples(0)
"""
if not (0 <= trace_index < self.num_traces()):
raise ValueError("Trace index {} out of range".format(trace_index))
pos = self._trace_offset_catalog[trace_index]
trace_header = read_trace_header(self._fh, self._trace_header_format, pos)
return trace_header
@property
def dimensionality(self):
"""The spatial dimensionality of the data.
Returns:
3 for 3D seismic volumes, 2 for 2D seismic lines, 1 for a
single trace_samples, otherwise 0.
"""
return self._dimensionality()
def _dimensionality(self):
return 1 if self.num_traces() == 1 else 0
@property
def textual_reel_header(self):
"""The textual real header.
An immutable sequence of forty Unicode strings each 80 characters long.
"""
return self._textual_reel_header
@property
def binary_reel_header(self):
"""The binary reel header.
A dictionary containing data from the reel header.
"""
return self._binary_reel_header
@property
def extended_textual_header(self):
"""A sequence of sequences of Unicode strings.
If there were no headers, the sequence will be empty.
"""
return self._extended_textual_headers
@property
def filename(self):
"""The filename.
Returns:
The filename if it could be determined, otherwise '<unknown>'
"""
return filename_from_handle(self._fh)
@property
def revision(self):
"""The SEG Y revision.
Returns:
Either datatypes.SEGY_REVISION_0 or datatypes.SEGY_REVISION_1
"""
return self._revision
@property
def bytes_per_sample(self):
"""The number of bytes per trace_samples sample.
"""
return self._bytes_per_sample
@property
def data_sample_format(self):
"""The data type of the samples in machine-readable form.
Returns:
One of the values from datatypes.DATA_SAMPLE_FORMAT
"""
return DATA_SAMPLE_FORMAT[self._binary_reel_header['DataSampleFormat']]
@property
def data_sample_format_description(self):
"""A descriptive human-readable description of the data sample format
"""
return CTYPE_DESCRIPTION[self.data_sample_format]
@property
def encoding(self):
"""The encoding, of the data in the underlying file. Either ASCII ('ascii'),
EBCDIC ('cp037') or None."""
return self._encoding
@property
def endian(self):
"""The endianness of the data in the underlying file. Either '>' for big-endian or '<' for
little endian or None."""
return self._endian
class SegYReader3D(SegYReader):
"""A reader for 3D seismic data.
In addition to the capabilities provided by the SegYReader base
class, this reader provides an index to facilitate random access
to individual traces via crossline and inline co-ordinates.
"""
def __init__(self,
fh,
textual_reel_header,
binary_reel_header,
extended_textual_headers,
trace_offset_catalog,
trace_length_catalog,
line_catalog,
encoding,
endian='>'):
"""Initialize a SegYReader3D around a file-like-object.
Note:
Usually a SegYReader is most easily constructed using the
create_reader() function.
Args:
fh: A file-like object, which must support seeking and
support binary reading.
binary_reel_header: A dictionary containing reel header data.
trace_offset_catalog: A mapping from zero-based trace_samples indexes to
the byte-offset to individual traces within the file.
trace_length_catalog: A mapping from zero-based trace_samples indexes to
the number of samples in that trace_samples.
line_catalog: A mapping from (xline, inline) tuples to
trace_indexes.
encoding: Either ASCII or EBCDIC.
endian: '>' for big-endian data (the standard and default), '<' for
little-endian (non-standard)
"""
super(SegYReader3D, self).__init__(fh, textual_reel_header, binary_reel_header, extended_textual_headers,
trace_offset_catalog, trace_length_catalog, encoding, endian)
self._line_catalog = line_catalog
self._num_inlines = None
self._num_xlines = None
def _dimensionality(self):
return 3
def inline_range(self):
"""A range encompassing inline numbers.
The number of inlines within this range can be found with len(reader.inline_range()).
Returns:
A range() object with start set to the first inline number and stop set to
one beyond the last inline number. The range always has a step of one, although
this should not be taken as meaning that any intermediate inline number generated
by the range is valid.
"""
start = self._line_catalog.key_min()[0]
stop = self._line_catalog.key_max()[0] + 1
return range(start, stop)
def num_inlines(self):
"""The number of distinct inlines in the survey.
This number is not necessarily the same as the value returned by
len(reader.inline_range()) as there may be missing inlines within the range.
"""
if self._num_inlines is None:
try:
self._num_inlines = self._line_catalog.i_max - self._line_catalog.i_min + 1
except AttributeError:
self._num_inlines = len(set(i for i, j in self._line_catalog))
return self._num_inlines
def xline_range(self):
"""A range encompassing crossline numbers.
The number of crosslines within this range can be found with len(reader.crossline_range()).
Returns:
A range() object with start set to the first crossline number and stop set to
one beyond the last crossline number. The range always has a step of one, although
this should not be taken as meaning that any intermediate crossline number generated
by the range is valid.
"""
start = self._line_catalog.key_min()[1]
stop = self._line_catalog.key_max()[1] + 1
return range(start, stop)
def num_xlines(self):
"""The number of distinct crosslines in the survey.
This number is not necessarily the same as the value returned by
len(reader.xline_range()) as there may be missing crosslines within the range.
"""
if self._num_xlines is None:
try:
self._num_xlines = self._line_catalog.j_max - self._line_catalog.j_min + 1
except AttributeError:
self._num_xlines = len(set(j for i, j in self._line_catalog))
return self._num_xlines
def inline_xline_numbers(self):
"""An iterator over all (inline_number, xline_number) tuples
corresponding to traces.
"""
return iter(self._line_catalog)
def has_trace_index(self, inline_xline):
"""Determine whether a specific trace_samples exists.
Args:
inline_xline: A 2-tuple of inline number, crossline number.
Returns:
True if the specified trace_samples exists, otherwise False.
"""
return inline_xline in self._line_catalog
def trace_index(self, inline_xline):
"""Obtain the trace_samples index given an xline and a inline.
Note:
Do not assume that all combinations of crossline and
inline co-ordinates are valid. The volume may not be
rectangular. Valid values can be obtained from the
inline_xline_numbers() iterator.
Furthermore, inline and crossline numbers should not be
relied upon to be zero- or one-based indexes (although
they may be).
Args:
inline_xline: A 2-tuple of inline number, crossline number.
Returns:
A trace_samples index which can be used with trace_samples().
"""
return self._line_catalog[inline_xline]
class SegYReader2D(SegYReader):
def __init__(self,
fh,
textual_reel_header,
binary_reel_header,
extended_textual_headers,
trace_offset_catalog,
trace_length_catalog,
cdp_catalog,
encoding,
endian='>'):
"""Initialize a SegYReader2D around a file-like-object.
Note:
Usually a SegYReader is most easily constructed using the
create_reader() function.
Args:
fh: A file-like object, which must support seeking and
support binary reading.
binary_reel_header: A dictionary containing reel header data.
trace_catalog_offset: A mapping from zero-based trace_samples index to
the byte-offset to individual traces within the file.
trace_length_catalog: A mapping from zero-based trace_samples indexes to
the number of samples in that trace_samples.
cdp_catalog: A mapping from CDP numbers to trace_indexes.
encoding: Either ASCII or EBCDIC.
endian: '>' for big-endian data (the standard and default), '<' for
little-endian (non-standard)
"""
super(SegYReader2D, self).__init__(fh, textual_reel_header, binary_reel_header, extended_textual_headers,
trace_offset_catalog, trace_length_catalog, encoding, endian)
self._cdp_catalog = cdp_catalog
def _dimensionality(self):
return 2
def cdp_numbers(self):
"""An iterator over all cdp numbers corresponding to traces.
"""
return iter(self._cdp_catalog)
def cdp_range(self):
"""A range encompassing CDP numbers.
The number of CDPs within this range can be found with len(reader.cdp_range()).
Returns:
A range() object with start set to the first CDP number and stop set to
one beyond the last CDP number. The range always has a step of one, although
this should not be taken as meaning that any intermediate CDP number generated
by the range is valid.
"""
start = self._cdp_catalog.value_min()
stop = self._cdp_catalog.value_max() + 1
return range(start, stop)
def num_cdps(self):
"""The number of distinct CDPs.
This number is not necessarily the same as the value returned by
len(reader.cdp_range()) as there may be missing CDPs.
"""
return len(self._cdp_catalog)
def has_trace_index(self, cdp_number):
"""Determine whether a specified trace_samples exists.
Args:
cdp_number: A CDP number.
Returns:
True if the trace_samples exists, otherwise False.
"""
return self._cdp_catalog[cdp_number]
def trace_index(self, cdp_number):
"""Obtain the trace_samples index given an xline and a inline.
Args:
cdp_number: A CDP number.
Returns:
A trace_samples index which can be used with trace_samples().
"""
return self._cdp_catalog[cdp_number]
def main(argv=None):
import sys
if argv is None:
argv = sys.argv[1:]
class ProgressBar(object):
def __init__(self, num_chars, character='.'):
self._num_chars = num_chars
self._character = character
self._ratchet = 0
def __call__(self, proportion):
existing = self._num_marks(self._ratchet)
required = self._num_marks(proportion)
print(self._character * (required - existing), end='')
self._ratchet = proportion
def _num_marks(self, p):
return int(round(p * self._num_chars))
filename = argv[0]
with open(filename, 'rb') as segy_file:
segy_reader = create_reader(segy_file, progress=ProgressBar(30))
print()
print("Filename: ", segy_reader.filename)
print("SEG Y revision: ", segy_reader.revision)
print("Number of traces: ", segy_reader.num_traces())
print("Data format: ",
segy_reader.data_sample_format_description)
print("Dimensionality: ", segy_reader.dimensionality)
try:
print("Number of CDPs: ", segy_reader.num_cdps())
except AttributeError:
pass
try:
print("Number of inlines: ", segy_reader.num_inlines())
print("Number of crosslines: ", segy_reader.num_xlines())
except AttributeError:
pass
print("=== BEGIN TEXTUAL REEL HEADER ===")
for line in segy_reader.textual_reel_header:
print(line[3:])
print("=== END TEXTUAL REEL HEADER ===")
print()
print("=== BEGIN EXTENDED TEXTUAL HEADER ===")
print(segy_reader.extended_textual_header)
print("=== END EXTENDED TEXTUAL_HEADER ===")
for trace_index in segy_reader.trace_indexes():
trace_header = segy_reader.trace_header(trace_index)
print("Inline {}, Crossline {}, Shotpoint {}".format(trace_header.Inline3D, trace_header.Crossline3D,
trace_header.ShotPoint))
if __name__ == '__main__':
main()
revisions.py → segpy/revisions.py
+6 -3
View File
@@ -1,15 +1,18 @@
SEGY_REVISION_0 = 0x0000
SEGY_REVISION_1 = 0x0100
SEGY_REVISION_0 = 0
SEGY_REVISION_1 = 1
VARIANTS = {SEGY_REVISION_0: SEGY_REVISION_0,
SEGY_REVISION_1: SEGY_REVISION_1,
0: SEGY_REVISION_0,
1: SEGY_REVISION_1,
100: SEGY_REVISION_1,
256: SEGY_REVISION_1}
class SegYRevisionError(Exception):
pass
def canonicalize_revision(revision):
"""Canonicalize a SEG Y revision.
segpy/textual_reel_header_definition.py
+147
View File
@@ -0,0 +1,147 @@
from segpy.revisions import SEGY_REVISION_0, SEGY_REVISION_1
TEMPLATE = """
C 1 CLIENT { client } COMPANY { company } CREW NO {crew }
C 2 LINE { line } AREA { area } MAP ID { map_id }
C 3 REEL NO {reelnum} DAY-START OF REEL {d} YEAR {yr} OBSERVER {observer }
C 4 INSTRUMENT: MFG { mfg } MODEL { model } SERIAL NO { serial }
C 5 DATA TRACES/RECORD {dtpr} AUXILIARY TRACES/RECORD {atpr } CDP FOLD {cdpfold}
C 6 SAMPLE INTERVAL {intvl} SAMPLES/TRACE {spt} BITS/IN {bi} BYTES/SAMPLE {bps }
C 7 RECORDING FORMAT {rfmt} FORMAT THIS REEL {ftr } MEASUREMENT SYSTEM {measmnt}
C 8 SAMPLE CODE: FLOATING PT {f} FIXED PT {x} FIXED PT-GAIN {g} CORRELATED {cor}
C 9 GAIN TYPE: FIXED {i} BINARY {b} FLOATING POINT {c} OTHER {other }
C10 FILTERS: ALIAS {a }HZ NOTCH {n }HZ BAND {b1}-{b2 }HZ SLOPE {s}-{s2}DB/OCT
C11 SOURCE: TYPE {type } NUMBER/POINT {npt } POINT INTERVAL {point_interval }
C12 PATTERN: {source_pattern } LENGTH {lent} WIDTH {width }
C13 SWEEP: START {ss}HZ END {se}HZ LENGTH {lms}MS CHANNEL NO {q} TYPE {cd }
C14 TAPER: START LENGTH {tsl }MS END LENGTH {tel }MS TYPE {taper_type }
C15 SPREAD: OFFSET {off } MAX DISTANCE {md } GROUP INTERVAL {group_interval }
C16 GEOPHONES: PER GROUP {p} SPACING {y} FREQUENCY {r} MFG {gmfg } MODEL {gmod}
C17 PATTERN: {geophone_pattern } LENGTH {glen} WIDTH {geophone_width }
C18 TRACES SORTED BY: RECORD {u} CDP {v} OTHER { sort_other }
C19 AMPLITUDE RECOVERY: NONE {ar} SPHERICAL DIV {sd } AGC {} OTHER {ar_other }
C20 MAP PROJECTION {map_projection } ZONE ID {zid} COORDINATE UNITS {co_units }
C21 PROCESSING: { processing1 }
C22 PROCESSING: { processing2 }
C23 { unassigned1 }
C24 { unassigned2 }
C25 { unassigned3 }
C26 { unassigned4 }
C27 { unassigned5 }
C28 { unassigned6 }
C29 { unassigned7 }
C30 { unassigned8 }
C31 { unassigned9 }
C32 { unassigned10 }
C33 { unassigned11 }
C34 { unassigned12 }
C35 { unassigned13 }
C36 { unassigned14 }
C37 { unassigned15 }
C38 { unassigned16 }
C39 { unassigned17 }
C40 { end_marker }
"""
END_TEXTUAL_HEADER = 'END TEXTUAL HEADER'
END_EBCDIC = 'END EBCDIC'
END_MARKERS = {SEGY_REVISION_0: END_EBCDIC,
SEGY_REVISION_1: END_TEXTUAL_HEADER}
TEMPLATE_FIELD_NAMES = {'client': 'client',
'company': 'company',
'crew': 'crew_number',
'line': 'line',
'area': 'area',
'map_id': 'map_id',
'reelnum': 'reel_number',
'd': 'day_start_of_reel',
'yr': 'year',
'observer': 'observer',
'mfg': 'instrument_manufacturer',
'model': 'instrument_model',
'serial': 'instrument_serial',
'dtpr': 'data_traces_per_record',
'atpr': 'auxiliary_traces_per_record',
'cdpfold': 'cdp_fold',
'intvl': 'sample_interval',
'spt': 'samples_per_trace',
'bi': 'bits_per_inch',
'bps': 'bytes_per_sample',
'rfmt': 'recording_format',
'ftr': 'format_this_reel',
'measmnt': 'measurement_system',
'f': 'sample_code_floating_point',
'x': 'sample_code_fixed_point',
'g': 'sample_code_fixed_point_gain',
'cor': 'sample_code_correlated',
'i': 'gain_type_fixed',
'b': 'gain_type_binary',
'c': 'gain_type_fixed_point_gain',
'other': 'gain_type_other',
'a': 'filters_alias_hz',
'n': 'filters_notch_hz',
'b1': 'filters_band_lower_hz',
'b2': 'filters_band_upper_hz',
's': 'filters_slope_lower_db_per_oct',
's2': 'filters_slope_upper_db_per_oct',
'type': 'source_type',
'npt': 'source_number_per_point',
'point_interval': 'source_point_interval',
'source_pattern': 'source_pattern',
'lent': 'source_length',
'width': 'source_width',
'ss': 'sweep_start_hz',
'se': 'sweep_end_hz',
'lms': 'sweep_length_ms',
'q': 'sweep_channel_number',
'cd': 'sweep_type',
'tsl': 'taper_start_length_ms',
'tel': 'taper_end_length_ms',
'taper_type': 'taper_type',
'off': 'spread_offset',
'md': 'spread_max_distance',
'group_interval': 'spread_group_interval',
'p': 'geophones_per_group',
'y': 'geophone_spacing',
'r': 'geophone_frequency',
'gmfg': 'geophone_manufacturer',
'gmod': 'geophone_model',
'geophone_pattern': 'geophone_pattern',
'glen': 'geophone_length',
'geophone_width': 'geophone_width',
'u': 'traces_sorted_by_record',
'v': 'traces_sorted_by_cdp',
'sort_other': 'traces_sorted_by_other',
'ar': 'amplitude_recovery_none',
'sd': 'amplitude_recovery_spherical_div',
'': 'amplitude_recovery_agc',
'ar_other': 'amplitude_recovery_other',
'map_projection': 'map_projection',
'zid': 'zone_id',
'co_units': 'coordinate_units',
'processing1': 'processing1',
'processing2': 'processing2',
'unassigned1': 'unassigned1',
'unassigned2': 'unassigned2',
'unassigned3': 'unassigned3',
'unassigned4': 'unassigned4',
'unassigned5': 'unassigned5',
'unassigned6': 'unassigned6',
'unassigned7': 'unassigned7',
'unassigned8': 'unassigned8',
'unassigned9': 'unassigned9',
'unassigned10': 'unassigned10',
'unassigned11': 'unassigned11',
'unassigned12': 'unassigned12',
'unassigned13': 'unassigned13',
'unassigned14': 'unassigned14',
'unassigned15': 'unassigned15',
'unassigned16': 'unassigned16',
'unassigned17': 'unassigned17',
'end_marker': 'end_marker'
}
INV_TEMPLATE_FIELD_NAMES = dict((v, k) for k, v in TEMPLATE_FIELD_NAMES.items())
segpy/toolkit.py
+899
View File
@@ -0,0 +1,899 @@
from __future__ import print_function
from array import array
from collections import namedtuple, OrderedDict
import itertools
import os
import struct
import re
import logging
from segpy import textual_reel_header_definition
from segpy.catalog import CatalogBuilder
from segpy.datatypes import CTYPES, size_in_bytes
from segpy.encoding import guess_encoding, is_supported_encoding, UnsupportedEncodingError
from segpy.binary_reel_header_definition import HEADER_DEF
from segpy.ibm_float import IBMFloat
from segpy.revisions import canonicalize_revision
from segpy.trace_header_definition import TRACE_HEADER_DEF
from segpy.util import file_length, batched, pad, complementary_intervals, NATIVE_ENDIANNESS
from segpy.portability import EMPTY_BYTE_STRING, izip_longest
HEADER_NEWLINE = '\r\n'
CARD_LENGTH = 80
CARDS_PER_HEADER = 40
TEXTUAL_HEADER_NUM_BYTES = CARD_LENGTH * CARDS_PER_HEADER
BINARY_HEADER_NUM_BYTES = 400
REEL_HEADER_NUM_BYTES = TEXTUAL_HEADER_NUM_BYTES + BINARY_HEADER_NUM_BYTES
TRACE_HEADER_NUM_BYTES = 240
END_TEXT_STANZA = "((SEG: EndText))"
def logger():
# Defer logger creation until the module is *used* rather than imported.
return logging.getLogger(__name__)
def extract_revision(binary_reel_header):
"""Obtain the SEG Y revision from the reel header.
Args:
binary_reel_header: A dictionary containing a reel header, such as obtained
from read_binary_reel_header()
Returns:
One of the constants revisions.SEGY_REVISION_0 or
revisions.SEGY_REVISION_1
"""
raw_revision = binary_reel_header['SegyFormatRevisionNumber']
return canonicalize_revision(raw_revision)
def num_extended_textual_headers(binary_reel_header):
"""Obtain the number of 3200 byte extended textual file headers.
A value of zero indicates there are no Extended Textual File Header records
(i.e. this file has no Extended Textual File Header(s)). A value of -1 indicates
that there are a variable number of Extended Textual File Header records and the
end of the Extended Textual File Header is denoted by an ((SEG: EndText)) stanza
in the final record. A positive value indicates that there are exactly that many
Extended Textual File Header records.
"""
num_ext_headers = binary_reel_header['NumberOfExtTextualHeaders']
return num_ext_headers
def bytes_per_sample(binary_reel_header, revision):
"""Determine the number of bytes per sample from the reel header.
Args:
binary_reel_header: A dictionary containing a reel header, such as obtained
from read_binary_reel_header()
revision: One of the constants revisions.SEGY_REVISION_0 or
revisions.SEGY_REVISION_1
Returns:
An integer number of bytes per sample.
"""
dsf = binary_reel_header['DataSampleFormat']
bps = HEADER_DEF["DataSampleFormat"]["bps"][revision][dsf]
return bps
def samples_per_trace(binary_reel_header):
"""Determine the number of samples per trace_samples from the reel header.
Note: There is no requirement for all traces to be of the same length,
so this value should be considered indicative only, and as such is
mostly useful in the absence of other information. The actual number
of samples for a specific trace_samples should be retrieved from individual
trace_samples headers.
Args:
binary_reel_header: A dictionary containing a reel header, such as obtained
from read_binary_reel_header()
Returns:
An integer number of samples per trace_samples
"""
return binary_reel_header['ns']
def trace_length_bytes(binary_reel_header, bps):
"""Determine the trace_samples length in bytes from the reel header.
Note: There is no requirement for all traces to be of the same length,
so this value should be considered indicative only, and as such is
mostly useful in the absence of other information. The actual number
of samples for a specific trace_samples should be retrieved from individual
trace_samples headers.
Args:
binary_reel_header: A dictionary containing a reel header, such as obtained
from read_binary_reel_header()
bps: The number of bytes per sample, such as obtained from a call to
bytes_per_sample()
"""
return samples_per_trace(binary_reel_header) * bps + TRACE_HEADER_NUM_BYTES
def guess_textual_header_encoding(fh):
fh.seek(0)
raw_header = fh.read(TEXTUAL_HEADER_NUM_BYTES)
encoding = guess_encoding(raw_header)
return encoding
def read_textual_reel_header(fh, encoding):
"""Read the SEG Y card image header, also known as the textual header
Args:
fh: A file-like object open in binary mode positioned such that the
beginning of the textual header will be the next byte to read.
encoding: Either 'cp037' for EBCDIC or 'ascii' for ASCII.
Returns:
A tuple of forty Unicode strings (Python 2: unicode, Python 3: str)
containing the transcoded header data.
"""
fh.seek(0)
raw_header = fh.read(TEXTUAL_HEADER_NUM_BYTES)
num_bytes_read = len(raw_header)
if num_bytes_read < TEXTUAL_HEADER_NUM_BYTES:
raise EOFError("Only {} bytes of {} byte textual reel header could be read"
.format(num_bytes_read, TEXTUAL_HEADER_NUM_BYTES))
lines = tuple(bytes(raw_line).decode(encoding) for raw_line in batched(raw_header, CARD_LENGTH))
return lines
def read_binary_reel_header(fh, endian='>'):
"""Read the SEG Y binary reel header.
Args:
fh: A file-like object open in binary mode. Binary header is assumed to
be at an offset of 3200 bytes from the beginning of the file.
endian: '>' for big-endian data (the standard and default), '<' for
little-endian (non-standard)
"""
fh.seek(TEXTUAL_HEADER_NUM_BYTES)
reel_header = {}
for key in HEADER_DEF:
pos = HEADER_DEF[key]['pos']
ctype = HEADER_DEF[key]['type']
values = tuple(read_binary_values(fh, pos, ctype, 1, endian))
reel_header[key] = values[0]
return reel_header
def has_end_text_stanza(ext_header):
"""Determine whether the header is the end text stanza.
Args:
ext_header: A sequence of forty CARD_LENGTH character Unicode strings.
Returns:
True if the header is the SEG Y Revision 1 end text header,
otherwise False.
"""
return END_TEXT_STANZA in ext_header[0]
def read_extended_headers_until_end(fh, encoding):
"""Read an unspecified number of extended textual headers, until the end-text header is found.
Args:
fh: A file-like object open in binary mode. The first of any extended textual headers
is assumed to be at an offset of 3600 bytes from the beginning of the file
(immediately following the binary reel header).
encoding: Optional encoding of the header in the file. If None (the
default) a reliable heuristic will be used to guess the encoding.
Typically 'cp037' for EBCDIC or 'ascii' for ASCII.
Returns:
A list of tuples each containing forty CARD_LENGTH character Unicode strings. If present, the end_text
stanza is excluded.
"""
extended_headers = []
while True:
ext_header = read_textual_reel_header(fh, encoding)
extended_headers.append(ext_header)
if has_end_text_stanza(ext_header):
break
return extended_headers
def read_extended_headers_counted(fh, num_expected, encoding):
"""Read a specified number of extended textual headers.
If an end-text stanza is located prematurely (in anything other than the last expected header)
reading will be terminated and a warning logged.
Args:
fh: A file-like object open in binary mode. The first of any extended textual headers
is assumed to be at an offset of 3600 bytes from the beginning of the file
(immediately following the binary reel header).
num_expected: A non-negative integer of headers.
encoding: Optional encoding of the header in the file. If None (the
default) a reliable heuristic will be used to guess the encoding.
Typically 'cp037' for EBCDIC or 'ascii' for ASCII.
Returns:
A list of tuples each containing forty CARD_LENGTH -character Unicode strings.
"""
assert num_expected >= 0
extended_headers = []
for i in range(num_expected):
ext_header = read_textual_reel_header(fh, encoding)
if has_end_text_stanza(ext_header):
if i != num_expected - 1:
logger().warning("Unexpected end-text extended header.")
break
extended_headers.append(ext_header)
return extended_headers
def read_extended_textual_headers(fh, binary_reel_header, encoding):
"""Read any extended textual reel headers.
Args:
fh: A file-like object open in binary mode. The first of any extended textual headers
is assumed to be at an offset of 3600 bytes from the beginning of the file
(immediately following the binary reel header).
binary_reel_header: A dictionary containing data read from the binary
reel header by the read_binary_reel_header() function.
encoding: Optional encoding of the header in the file. If None (the
default) a reliable heuristic will be used to guess the encoding.
Typically 'cp037' for EBCDIC or 'ascii' for ASCII.
Returns:
A sequence of sequences of Unicode strings representing headers of lines of characters. The length of the
outer sequence will be equal to the number of extended headers read. Each item in the outer sequence will be
a sequence of exactly forty Unicode strings. To combine the headers into a single string, consider using
concatenate_extended_textual_headers().
Post-condition:
As a post-condition to this function, the file-pointer of fh will be
positioned immediately after the last extended textual header, which
should be the start of the first trace_samples header.
"""
fh.seek(REEL_HEADER_NUM_BYTES)
declared_num_ext_headers = num_extended_textual_headers(binary_reel_header)
if declared_num_ext_headers < 0:
return read_extended_headers_until_end(fh, encoding)
return read_extended_headers_counted(fh, declared_num_ext_headers, encoding)
_READ_PROPORTION = 0.75 # The proportion of time spent in catalog_traces
# reading the file. Determined empirically.
def catalog_traces(fh, bps, endian='>', progress=None):
"""Build catalogs to facilitate random access to trace_samples data.
Note:
This function can take significant time to run, proportional
to the number of traces in the SEG Y file.
Four catalogs will be build:
1. A catalog mapping trace_samples index (0-based) to the position of that
trace_samples header in the file.
2. A catalog mapping trace_samples index (0-based) to the number of
samples in that trace_samples.
3. A catalog mapping CDP number to the trace_samples index.
4. A catalog mapping an (inline, crossline) number 2-tuple to
trace_samples index.
Args:
fh: A file-like-object open in binary mode, positioned at the
start of the first trace_samples header.
bps: The number of bytes per sample, such as obtained by a call
to bytes_per_sample()
endian: '>' for big-endian data (the standard and default), '<'
for little-endian (non-standard)
progress: A unary callable which will be passed a number
between zero and one indicating the progress made. If
provided, this callback will be invoked at least once with
an argument equal to 1
Returns:
A 4-tuple of the form (trace_samples-offset-catalog,
trace_samples-length-catalog,
cdp-catalog,
line-catalog)` where
each catalog is an instance of ``collections.Mapping`` or None
if no catalog could be built.
"""
progress_callback = progress if progress is not None else lambda p: None
if not callable(progress_callback):
raise TypeError("catalog_traces(): progress callback must be callable")
trace_header_format = compile_trace_header_format(endian)
length = file_length(fh)
pos_begin = fh.tell()
trace_offset_catalog_builder = CatalogBuilder()
trace_length_catalog_builder = CatalogBuilder()
line_catalog_builder = CatalogBuilder()
alt_line_catalog_builder = CatalogBuilder()
cdp_catalog_builder = CatalogBuilder()
for trace_number in itertools.count():
progress_callback(_READ_PROPORTION * pos_begin / length)
fh.seek(pos_begin)
data = fh.read(TRACE_HEADER_NUM_BYTES)
if len(data) < TRACE_HEADER_NUM_BYTES:
break
trace_header = TraceHeader._make(trace_header_format.unpack(data))
num_samples = trace_header.ns
trace_length_catalog_builder.add(trace_number, num_samples)
samples_bytes = num_samples * bps
trace_offset_catalog_builder.add(trace_number, pos_begin)
# Should we check the data actually exists?
line_catalog_builder.add((trace_header.Inline3D,
trace_header.Crossline3D),
trace_number)
alt_line_catalog_builder.add((trace_header.TraceSequenceFile,
trace_header.cdp),
trace_number)
cdp_catalog_builder.add(trace_header.cdp, trace_number)
pos_end = pos_begin + TRACE_HEADER_NUM_BYTES + samples_bytes
pos_begin = pos_end
progress_callback(_READ_PROPORTION)
trace_offset_catalog = trace_offset_catalog_builder.create()
progress_callback(_READ_PROPORTION + (_READ_PROPORTION / 4))
trace_length_catalog = trace_length_catalog_builder.create()
progress_callback(_READ_PROPORTION + (_READ_PROPORTION / 2))
cdp_catalog = cdp_catalog_builder.create()
progress_callback(_READ_PROPORTION + (_READ_PROPORTION * 3 / 4))
line_catalog = line_catalog_builder.create()
if line_catalog is None:
# Some 3D files put Inline and Crossline numbers in (TraceSequenceFile, cdp) pair
line_catalog = alt_line_catalog_builder.create()
progress_callback(1)
return (trace_offset_catalog,
trace_length_catalog,
cdp_catalog,
line_catalog)
def read_trace_header(fh, trace_header_format, pos=None):
"""Read a trace_samples header.
Args:
fh: A file-like-object open in binary mode.
trace_header_format: A Struct object, such as obtained from a
call to compile_trace_header_format()
pos: The file offset in bytes from the beginning from which the data
is to be read.
Returns:
A TraceHeader object.
"""
if pos is not None:
fh.seek(pos)
data = fh.read(TRACE_HEADER_NUM_BYTES)
trace_header = TraceHeader._make(
trace_header_format.unpack(data))
return trace_header
def read_binary_values(fh, pos=None, ctype='int32', count=1, endian='>'):
"""Read a series of values from a binary file.
Args:
fh: A file-like-object open in binary mode.
c
ctype: The SEG Y data type.
number: The number of items to be read.
Returns:
A sequence containing count items.
"""
fmt = CTYPES[ctype]
item_size = size_in_bytes(fmt)
block_size = item_size * count
fh.seek(pos, os.SEEK_SET)
buf = fh.read(block_size)
if len(buf) < block_size:
raise EOFError("{} bytes requested but only {} available".format(
block_size, len(buf)))
values = (unpack_ibm_floats(buf, count)
if fmt == 'ibm'
else unpack_values(buf, count, fmt, endian))
assert len(values) == count
return values
def unpack_ibm_floats(data, count):
"""Unpack a series of binary-encoded big-endian single-precision IBM floats.
Args:
data: A sequence of bytes. (Python 2 - a str object,
Python 3 - a bytes object)
count: The number of floats to be read.
Returns:
A sequence of floats.
"""
return [IBMFloat.from_bytes(data[i: i+4]) for i in range(0, count * 4, 4)]
def unpack_values(buf, count, fmt, endian='>'):
"""Unpack a series items from a byte string.
Args:
data: A sequence of bytes. (Python 2 - a str object,
Python 3 - a bytes object)
count: The number of floats to be read.
fmt: A format code (one of the values in the datatype.CTYPES
dictionary)
endian: '>' for big-endian data (the standard and default), '<'
for little-endian (non-standard)
Returns:
A sequence of objects with type corresponding to the format code.
"""
a = array(fmt, buf)
if endian != NATIVE_ENDIANNESS:
a.byteswap()
return a
def format_standard_textual_header(revision, **kwargs):
"""Produce a standard SEG Y textual header.
Args:
revision: The SEG Y revision.
**kwargs: Named arguments corresponding to the values in the
textual_reel_header_definition.TEMPLATE_FIELD_NAMES dictionary,
which in turn correspond to the placeholders in the
textual_reel_header_definition.TEMPLATE string. Any omitted
arguments will result in placeholders being replaced by spaces.
If the end_marker argument is not supplied, an appropriate end
marker will be selected based on the SEG Y revision. For standard
end markers consider using textual_reel_header_definition.END_TEXTUAL_HEADER
or textual_reel_header_definition.END_EBCDIC.
Returns:
A list of forty Unicode strings.
Usage:
header = format_standard_textual_header(1,
client="Lundin",
company="Western Geco",
crew_number=123,
processing1="Sixty North AS",
sweep_start_hz=10,
sweep_end_hz=1000,
sweep_length_ms=10000,
sweep_channel_number=3,
sweep_type='spread')
"""
kwargs.setdefault('end_marker', textual_reel_header_definition.END_MARKERS[revision])
template = textual_reel_header_definition.TEMPLATE
placeholder_slices = parse_template(template)
background_slices = complementary_intervals(placeholder_slices.values(), 0, len(template))
chunks = []
for bg_slice, placeholder in izip_longest(background_slices, placeholder_slices.items()):
if bg_slice is not None:
chunks.append(template[bg_slice])
if placeholder is not None:
ph_name, ph_slice = placeholder
ph_arg_name = textual_reel_header_definition.TEMPLATE_FIELD_NAMES[ph_name]
ph_value = kwargs.pop(ph_arg_name, '')
ph_len = ph_slice.stop - ph_slice.start
substitute = str(ph_value)[:ph_len].ljust(ph_len, ' ')
chunks.append(substitute)
if len(kwargs) > 0:
raise TypeError("The following keyword arguments did not correspond to template placeholders: {!r}"
.format(list(kwargs.keys())))
concatenation = ''.join(chunks)
lines = concatenation.splitlines(keepends=False)
return lines[1:] # Omit the first and last lines, which are artifacts of the multi-line string template
_TEMPLATE_PATTERN = r'\{\s*(\w*)\s*\}'
_TEMPLATE_REGEX = re.compile(_TEMPLATE_PATTERN)
def parse_template(template):
"""Parse a template to produce a dictionary of placeholders.
Args:
template: The template string containing { field-name } style fixed-width fields.
Returns:
A OrderedDict mapping field names to slices objects which can be used to index
into the template string. The order of the entries is the same as the order within
which they occur in the template.
"""
matches = _TEMPLATE_REGEX.finditer(template)
fields = OrderedDict()
for match in matches:
name = match.group(1)
start = match.start()
end = match.end()
fields[name] = slice(start, end)
return fields
def write_textual_reel_header(fh, lines, encoding):
"""Write the SEG Y card image header, also known as the textual header
Args:
fh: A file-like object open in binary mode positioned such that the
beginning of the textual header will be the next byte to read.
lines: An iterable series of forty lines, each of which must be a
Unicode string of CARD_LENGTH characters. The first three characters
of each line are often "C 1" to "C40" (as required by the SEG Y
standard) although this is not enforced by this function, since
many widespread SEG Y readers and writers do not adhere to this
constraint. To produce a SEG Y compliant series of header lines
consider using the format_standard_textual_header() function.
Any lines longer than CARD_LENGTH characters will be truncated without
warning. Any excess lines over CARDS_PER_HEADER will be discarded. Short
or omitted lines will be padded with spaces.
encoding: Typically 'cp037' for EBCDIC or 'ascii' for ASCII.
Post-condition:
The file pointer in fh will be positioned at the first byte following the textual
header.
Raises:
UnsupportedEncodingError: If encoding is neither EBCDIC nor ASCII.
UnicodeError: If the data provided in lines cannot be encoded with the encoding.
"""
if not is_supported_encoding(encoding):
raise UnsupportedEncodingError("Writing textual reel header", encoding)
fh.seek(0)
padded_lines = [line.encode(encoding).ljust(CARD_LENGTH, ' '.encode(encoding))[:CARD_LENGTH]
for line in pad(lines, padding='', size=CARDS_PER_HEADER)]
joined_header = EMPTY_BYTE_STRING.join(padded_lines)
assert len(joined_header) == 3200
fh.write(joined_header)
fh.seek(TEXTUAL_HEADER_NUM_BYTES)
def write_binary_reel_header(fh, binary_reel_header, endian='>'):
"""Write the binary_reel_header to the given file-like object.
Args:
fh: A file-like object open in binary mode for writing.
binary_reel_header: A dictionary of values using a subset of the keys
in binary_reel_header_definition.HEADER_DEF associated with
compatible values.
Post-condition:
The file pointer for fh will be positioned at the first byte following
the binary reel header.
"""
for key in HEADER_DEF:
pos = HEADER_DEF[key]['pos']
ctype = HEADER_DEF[key]['type']
value = binary_reel_header[key] if key in binary_reel_header else HEADER_DEF[key]['def']
write_binary_values(fh, [value], ctype, pos, endian)
fh.seek(REEL_HEADER_NUM_BYTES)
def format_extended_textual_header(text, encoding, include_text_stop=False):
"""Format a string into pages and line suitable for an extended textual header.
Args
text: An arbitrary text string. Any universal newlines will be preserved.
encoding: Either ASCII ('ascii') or EBCDIC ('cp037')
include_text_stop: If True, a text stop stanza header will be appended, otherwise not.
"""
if not is_supported_encoding(encoding):
raise UnsupportedEncodingError("Extended textual header", encoding)
# According to the standard: "The Extended Textual File Header consists of one or more 3200-byte records, each
# record containing 40 lines of textual card-image text." It goes on "... Each line in an Extended Textual File
# Header ends in carriage return and linefeed (EBCDIC 0D25 or ASCII 0D0A)." Given that we're dealing with fixed-
# length (80 byte) lines, this implies that we have 78 bytes of space into which we can encode the content of each
# line, which must be left-justified and padded with spaces.
width = CARD_LENGTH - len(HEADER_NEWLINE)
original_lines = text.splitlines()
# Split overly long lines (i.e. > 78) and pad too-short lines with spaces
lines = []
for original_line in original_lines:
padded_lines = (pad_and_terminate_header_line(original_line[i:i+width], width)
for i in range(0, len(original_line), width))
lines.extend(padded_lines)
pages = list(batched(lines, 40, pad_and_terminate_header_line('', width)))
if include_text_stop:
stop_page = format_extended_textual_header(END_TEXT_STANZA, encoding)[0]
pages.append(stop_page)
return pages
def pad_and_terminate_header_line(line, width):
return line.ljust(width, ' ') + HEADER_NEWLINE
def write_extended_textual_headers(fh, pages, encoding):
"""Write extended textual headers.
Args:
fh: A file-like object open in binary mode for writing.
pages: An iterables series of sequences of Unicode strings, where the outer iterable
represents 3200 byte pages, each comprised of a sequence of exactly 40 strings of nominally 80 characters
each. Although Unicode strings are accepted, and when encoded they should result in exact 80 bytes
sequences. To produce a valid data structure for pages, consider using format_extended_textual_header()
encoding: Either 'cp037' for EBCDIC or 'ascii' for ASCII.
Post-condition:
The file pointer in fh will be position at the first byte after the extended textual headers, which is
also the first byte of the first trace-header.
Raises:
ValueError: If the provided header data has the wrong shape.
UnicodeError: If the textual data could not be encoded into the specified encoding.
"""
if not is_supported_encoding(encoding):
raise UnsupportedEncodingError("Writing extended textual header", encoding)
fh.seek(REEL_HEADER_NUM_BYTES)
encoded_pages = []
for page_index, page in enumerate(pages):
encoded_page = []
# TODO: Share some of this code with writing the textual reel header.
for line_index, line in enumerate(page):
encoded_line = line.encode(encoding)
num_encoded_bytes = len(encoded_line)
if num_encoded_bytes != CARD_LENGTH:
raise ValueError("Extended textual header line {} of page {} at {} bytes is not "
"{} bytes".format(line_index, page_index, num_encoded_bytes, CARD_LENGTH))
encoded_page.append(encoded_line)
num_encoded_lines = len(encoded_page)
if num_encoded_lines != CARDS_PER_HEADER:
raise ValueError("Extended textual header page {} number of "
"lines {} is not {}".format(num_encoded_lines, CARDS_PER_HEADER))
encoded_pages.append(encoded_page)
for encoded_page in encoded_pages:
concatenated_page = EMPTY_BYTE_STRING.join(encoded_page)
assert(len(concatenated_page) == TEXTUAL_HEADER_NUM_BYTES)
fh.write(concatenated_page)
def write_trace_header(fh, trace_header, trace_header_format, pos=None):
"""Write a TraceHeader to file.
Args:
fh: A file-like object open in binary mode for writing.
trace_header: A TraceHeader object.
trace_header_format: A Struct object, such as obtained from a
call to compile_trace_header_format()
pos: An optional file offset in bytes from the beginning of the
file. Defaults to the current file position.
"""
if pos is not None:
fh.seek(pos, os.SEEK_SET)
buf = trace_header_format.pack(*trace_header)
fh.write(buf)
def write_trace_samples(fh, samples, ctype='l', pos=None, endian='>'):
"""Write a trace samples to a file
Args:
fh: A file-like-object open for writing in binary mode.
values: An iterable series of values.
ctype: The SEG Y data type.
pos: An optional offset from the beginning of the file. If omitted,
any writing is done at the current file position.
endian: '>' for big-endian data (the standard and default), '<'
for little-endian (non-standard)
"""
write_binary_values(fh, samples, ctype, pos, endian)
def write_binary_values(fh, values, ctype, pos=None, endian='>'):
"""Write a series of values to a file.
Args:
fh: A file-like-object open for writing in binary mode.
values: An iterable series of values.
ctype: The SEG Y data type.
pos: An optional offset from the beginning of the file. If omitted,
any writing is done at the current file position.
endian: '>' for big-endian data (the standard and default), '<'
for little-endian (non-standard)
"""
fmt = CTYPES[ctype]
if pos is not None:
fh.seek(pos, os.SEEK_SET)
buf = (pack_ibm_floats(values)
if fmt == 'ibm'
else pack_values(values, fmt, endian))
fh.write(buf)
def pack_ibm_floats(values):
"""Pack floats into binary-encoded big-endian single-precision IBM floats.
Args:
values: An iterable series of numeric values.
Returns:
A sequence of bytes. (Python 2 - a str object, Python 3 - a bytes
object)
"""
return EMPTY_BYTE_STRING.join(bytes(IBMFloat.from_real(value)) for value in values)
def pack_values(values, fmt, endian='>'):
"""Pack values into binary encoded big-endian byte strings.
Args:
values: An iterable series of values.
fmt: A format code (one of the values in the datatype.CTYPES
dictionary)
endian: '>' for big-endian data (the standard and default), '<'
for little-endian (non-standard)
"""
c_format = '{}{}{}'.format(endian, len(values), fmt)
return struct.pack(c_format, *values)
# TODO: Consider generalising the below to also produce a ReelHeader record. Then modify
# read_binary_reel_header() to return such a record, and write_binary_reel_header() to accept such
# a record.
_TraceAttributeSpec = namedtuple('Record', ['name', 'pos', 'type'])
def compile_trace_header_format(endian='>'):
"""Compile a format string for use with the struct module from the
trace_samples header definition.
Args:
endian: '>' for big-endian data (the standard and default), '<' for
little-endian (non-standard)
Returns:
A string which can be used with the struct module for parsing
trace_samples headers.
"""
record_specs = sorted(
[_TraceAttributeSpec(name,
TRACE_HEADER_DEF[name]['pos'],
TRACE_HEADER_DEF[name]['type'])
for name in TRACE_HEADER_DEF],
key=lambda r: r.pos)
fmt = [endian]
length = 0
for record_spec in record_specs:
shortfall = length - record_spec.pos
if shortfall:
fmt.append(str(shortfall) + 'x') # Ignore bytes
length += shortfall
ctype = CTYPES[record_spec.type]
fmt.append(ctype)
length += size_in_bytes(ctype)
assert length == TRACE_HEADER_NUM_BYTES
return struct.Struct(''.join(fmt))
def _compile_trace_header_record():
"""Build a TraceHeader namedtuple from the trace_samples header definition"""
record_specs = sorted(
[_TraceAttributeSpec(name,
TRACE_HEADER_DEF[name]['pos'],
TRACE_HEADER_DEF[name]['type'])
for name in TRACE_HEADER_DEF],
key=lambda r: r.pos)
return namedtuple('TraceHeader',
(record_spec.name for record_spec in record_specs))
TraceHeader = _compile_trace_header_record()
trace_header_definition.py → segpy/trace_header_definition.py
+1 -1
View File
@@ -1,4 +1,4 @@
from revisions import SEGY_REVISION_0, SEGY_REVISION_1
from segpy.revisions import SEGY_REVISION_0, SEGY_REVISION_1
TRACE_HEADER_DEF = {"TraceSequenceLine": {"pos": 0, "type": "int32"}}
TRACE_HEADER_DEF["TraceSequenceFile"] = {"pos": 4, "type": "int32"}
segpy/util.py
+240
View File
@@ -0,0 +1,240 @@
import itertools
import time
import os
import sys
from segpy.portability import izip
NATIVE_ENDIANNESS = '<' if sys.byteorder == 'little' else '>'
UNSET = object()
def pairwise(iterable):
"""Pairwise iteration.
Args:
iterable: An iterable series.
Returns:
An iterator over 2-tuples.
"""
a, b = itertools.tee(iterable)
next(b, None)
return izip(a, b)
def batched(iterable, batch_size, padding=UNSET):
"""Batch an iterable series into equal sized batches.
Args:
iterable: The series to be batched.
batch_size: The size of the batch. Must be at least one.
padding: Optional value used to pad the final batch to batch_size. If
omitted, the final batch may be smaller than batch_size.
Yields:
A series of lists, each containing batch_size items from iterable.
Raises:
ValueError: If batch_size is less than one.
"""
if batch_size < 1:
raise ValueError("Batch size {} is not at least one.".format(batch_size))
pending = []
for item in iterable:
pending.append(item)
if len(pending) == batch_size:
batch = pending
pending = []
yield batch
num_left_over = len(pending)
if num_left_over > 0:
if padding is not UNSET:
pending.extend([padding] * (batch_size - num_left_over))
yield pending
def pad(iterable, padding=None, size=None):
if size is None:
return itertools.chain(iterable, itertools.repeat(padding))
return itertools.islice(pad(iterable, padding), size)
def complementary_intervals(intervals, start=None, stop=None):
"""Compute a complementary set of intervals which alternate with given intervals to form a contiguous range.
Given,
Start Stop
[-----) [-----) [----)
produces,
[--) [----) [-) [---)
Args:
intervals: An sequence of at least one existing slices or ranges. The type of the first interval (slice or
range) is used as the result type.
start: An optional start index, defaults to the start of the first slice.
stop: An optional one-beyond-the-end index, defaults to the stop attribute of the last slice.
Yields:
A complementary series of slices which alternate with the supplied slices. The number of returned
slices will always be len(slices) + 1 since both leading and trailing slices will always be returned.
Note the some of the returned slices may be 'empty' (having zero length).
"""
if len(intervals) < 1:
raise ValueError("intervals must contain at least one interval (slice or range) object")
interval_type = type(intervals[0])
if start is None:
start = intervals[0].start
if stop is None:
stop = intervals[-1].stop
index = start
for s in intervals:
yield interval_type(index, s.start)
index = s.stop
yield interval_type(index, stop)
def roundrobin(*iterables):
"""Take items from each iterable in turn until all iterables are exhausted.
roundrobin('ABC', 'D', 'EF') --> A D E B F C
"""
# Recipe credited to George Sakkis
pending = len(iterables)
nexts = itertools.cycle(iter(it).__next__ for it in iterables)
while pending:
try:
for n in nexts:
yield n()
except StopIteration:
pending -= 1
nexts = itertools.cycle(itertools.islice(nexts, pending))
def contains_duplicates(sorted_iterable):
"""Determine in an iterable series contains duplicates.
Args:
sorted_iterable: Any iterable series which must be sorted in either
ascending or descending order.
Returns:
True if sorted_iterable contains duplicates, otherwise False.
"""
for a, b in pairwise(sorted_iterable):
if a == b:
return True
return False
def measure_stride(iterable):
"""Determine whether successive numeric items differ by a constant amount.
Args:
iterable: An iterable series of numeric values.
Returns:
The difference between successive values (e.g. item[1] - item[0]) if
that difference is the same between all successive pairs, otherwise
None.
"""
stride = None
for a, b in pairwise(iterable):
new_stride = b - a
if stride is None:
stride = new_stride
elif stride != new_stride:
return None
return stride
def minmax(iterable):
"""Return the minimum and maximum of an iterable series.
This function requires only a single pass over the data.
Args:
iterable: An iterable series for which to determine the minimum and
maximum values.
Returns:
A 2-tuple containing the minimum and maximum values.
"""
iterator = iter(iterable)
try:
first = next(iterator)
except StopIteration:
raise ValueError("minmax() arg is an empty iterable series")
minimum = first
maximum = first
for item in iterator:
minimum = min(minimum, item)
maximum = max(maximum, item)
return minimum, maximum
def file_length(fh):
"""Determine the length of a file-like object in bytes.
Args:
fh: A seekable file-like-object.
Returns:
An integer length in bytes.
"""
pos = fh.tell()
try:
fh.seek(0, os.SEEK_END)
return fh.tell()
finally:
fh.seek(pos, os.SEEK_SET)
def filename_from_handle(fh):
"""Determine the name of the file underlying a file-like object.
Args:
fh: A file-like object.
Returns:
A string containing the file name, or '<unknown>' if it could not
be determined.
"""
try:
return fh.name
except AttributeError:
return '<unknown>'
def now_millis():
millis = int(round(time.time() * 1000))
return millis
def round_up(integer, multiple):
"""Round up to the nearest multiple"""
return integer if integer % multiple == 0 else integer + multiple - integer % multiple
def underscores_to_camelcase(s):
"""Convert text_in_this_style to TextInThisStyle."""
return ''.join(w.capitalize() for w in s.split('_'))
def almost_equal(x, y, epsilon):
max_xy_one = max(1.0, abs(x), abs(y))
e = epsilon * max_xy_one
delta = abs(x - y)
return delta <= e
segpy/writer.py
+58
View File
@@ -0,0 +1,58 @@
from segpy.encoding import ASCII, is_supported_encoding, UnsupportedEncodingError
from segpy.toolkit import (write_textual_reel_header, write_binary_reel_header, compile_trace_header_format,
write_trace_header, write_trace_samples, format_extended_textual_header,
write_extended_textual_headers)
def write_segy(fh,
seg_y_data,
encoding=None,
endian='>',
progress=None):
"""
Args:
fh: A file-like object open for binary write.
seg_y_data: An object from which the headers and trace_samples data can be retrieved. Requires the following
properties and methods:
seg_y_data.textual_reel_header
seg_y_data.binary_reel_header
seg_y_data.extended_textual_header
seg_y_data.trace_indexes
seg_y_data.trace_header(trace_index)
seg_y_data.trace_samples(trace_index)
seg_y_data.encoding
seg_y_data.endian
One such legitimate object would be a SegYReader instance.
encoding: Optional encoding for text data. Typically 'cp037' for EBCDIC or 'ascii' for ASCII. If omitted, the
seg_y_data object will be queries for an encoding property.
endian: Big endian by default. If omitted, the seg_y_data object will be queried for an encoding property.
progress: An optional progress bar object.
Raises:
UnsupportedEncodingError: If the specified encoding is neither ASCII nor EBCDIC
UnicodeError: If textual data provided cannot be encoded into the required encoding.
"""
encoding = encoding or (hasattr(seg_y_data, 'encoding') and seg_y_data.encoding) or ASCII
if not is_supported_encoding(encoding):
raise UnsupportedEncodingError("Writing SEG Y", encoding)
write_textual_reel_header(fh, seg_y_data.textual_reel_header, encoding)
write_binary_reel_header(fh, seg_y_data.binary_reel_header, endian)
write_extended_textual_headers(fh, seg_y_data.extended_textual_header, encoding)
trace_header_format = compile_trace_header_format(endian)
for trace_index in seg_y_data.trace_indexes():
write_trace_header(fh, seg_y_data.trace_header(trace_index), trace_header_format)
write_trace_samples(fh, seg_y_data.trace_samples(trace_index), seg_y_data.data_sample_format, endian=endian)
segypy.py
-511
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@@ -1,511 +0,0 @@
"""
A Python module for reading/writing/manipulating
SEG-Y formatted files
segy.readSegy : Read SEGY file
segy.read_reel_header : Get SEGY header
segy.read_trace_header : Get SEGY Trace header
segy.read_all_trace_headers : Get all SEGY Trace headers
segy.getSegyTrace : Get SEGY Trace header and trace data for one trace
segy.writeSegy : Write a data to a SEGY file
segy.writeSegyStructure : Writes a segpy data structure to a SEGY file
segy.read_binary_value : Get a value from a binary string
segy.ibm2ieee : Convert IBM floats to IEEE
segy.version : The version of SegyPY
segy.verbose : Amount of verbose information to the screen
"""
#
# segpy : A Python module for reading and writing SEG-Y formatted data
#
# Forked by Robert Smallshire from the original segypy by
#
# (C) Thomas Mejer Hansen, 2005-2006
#
# with contributions from Pete Forman and Andrew Squelch 2007
import os
import sys
import struct
import logging
from numpy import (transpose, reshape, zeros, arange)
from revisions import canonicalize_revision
from header_definition import HEADER_DEF
from trace_header_definition import TRACE_HEADER_DEF
from ibm_float import ibm2ieee2
FORMAT = '%(asctime)-15s %(levelname)s %(message)s'
logging.basicConfig(level=logging.INFO, format=FORMAT)
logger = logging.getLogger('segpy.segypy')
version = '0.3.1'
REEL_HEADER_NUM_BYTES = 3600
TRACE_HEADER_NUM_BYTES = 240
l_char = struct.calcsize('c')
l_uchar = struct.calcsize('B')
l_float = struct.calcsize('f')
DATA_SAMPLE_FORMAT = {1: 'ibm',
2: 'l',
3: 'h',
5: 'f',
8: 'B'}
CTYPES = {'l': 'l', 'long': 'l', 'int32': 'l',
'L': 'L', 'ulong': 'L', 'uint32': 'L',
'h': 'h', 'short': 'h', 'int16': 'h',
'H': 'H', 'ushort': 'H', 'uint16': 'H',
'c': 'c', 'char': 'c',
'B': 'B', 'uchar': 'B',
'f': 'f', 'float': 'f',
'ibm': 'ibm'}
# TODO This is redundant with data in the SH_def below
CTYPE_DESCRIPTION = {'ibm': 'IBM float',
'l': '32 bit integer',
'h': '16 bit integer',
'f': 'IEEE float',
'B': '8 bit char'}
def size_in_bytes(ctype):
if ctype == 'l' and struct.calcsize(ctype) == 8:
return 4 # 64-bit issue?
return struct.calcsize(ctype) if ctype != 'ibm' else struct.calcsize('f')
def get_default_segy_header(ntraces=100, ns=100):
"""
header = getDefaultSegyHeader()
"""
# TraceSequenceLine
header = {'Job': {'pos': 3200, 'type': 'int32', 'def': 0}}
for key in HEADER_DEF:
header[key] = HEADER_DEF[key].get('def', 0)
header['ntraces'] = ntraces
header['ns'] = ns
return header
def get_default_segy_trace_headers(ntraces=100, ns=100, dt=1000):
"""
SH = getDefaultSegyTraceHeader()
"""
# INITIALIZE DICTIONARY
trace_header = {'TraceSequenceLine': {'pos': 0, 'type': 'int32'}}
for key in TRACE_HEADER_DEF:
trace_header[key] = zeros(ntraces)
for a in range(ntraces):
trace_header['TraceSequenceLine'][a] = a + 1
trace_header['TraceSequenceFile'][a] = a + 1
trace_header['FieldRecord'][a] = 1000
trace_header['TraceNumber'][a] = a + 1
trace_header['ns'][a] = ns
trace_header['dt'][a] = dt
return trace_header
def read_trace_header(f, reel_header, trace_header_name='cdp', endian='>'):
"""
read_trace_header(reel_header, TraceHeaderName)
"""
bps = get_byte_per_sample(reel_header)
# MAKE SOME LOOKUP TABLE THAT HOLDS THE LOCATION OF HEADERS
trace_header_pos = TRACE_HEADER_DEF[trace_header_name]['pos']
# TODO: Be consistent between 'type' and 'format' here.
trace_header_format = TRACE_HEADER_DEF[trace_header_name]['type']
ntraces = reel_header['ntraces']
trace_header_values = zeros(ntraces)
binary_reader = create_binary_reader(f, trace_header_format, endian)
start_pos = trace_header_pos + REEL_HEADER_NUM_BYTES
stride = reel_header['ns'] * bps + TRACE_HEADER_NUM_BYTES
end_pos = start_pos + (ntraces - 1) * stride + 1
for i, pos in enumerate(xrange(start_pos, end_pos, stride)):
trace_header_values[i] = binary_reader(pos)
return trace_header_values
# TODO: Get the parameter ordering of reel_header and f to be consistent
def read_all_trace_headers(f, reel_header):
trace_headers = {'filename': reel_header['filename']}
logger.debug('read_all_trace_headers : '
'trying to get all segy trace headers')
for key in TRACE_HEADER_DEF.keys():
trace_header = read_trace_header(f, reel_header, key)
trace_headers[key] = trace_header
logger.info("read_all_trace_headers : " + key)
return trace_headers
def file_length(f):
pos = f.tell()
f.seek(0, os.SEEK_END)
file_size = f.tell()
f.seek(pos, os.SEEK_SET)
return file_size
def _filename(f):
return f.name if hasattr(f, 'name') else '<unknown>'
def read_segy(f, endian='>'):
"""
data, header, trace_headers = read_reel_header(f)
"""
file_size = file_length(f)
logger.debug("read_segy : Length of data : {0}".format(file_size))
reel_header = read_reel_header(f, endian) # modified by A Squelch
# GET TRACE
index = REEL_HEADER_NUM_BYTES
bytes_per_sample = get_byte_per_sample(reel_header)
num_data = (file_size - REEL_HEADER_NUM_BYTES) / bytes_per_sample
data, reel_header, trace_headers = read_traces(f,
reel_header,
num_data,
bytes_per_sample,
index,
endian)
logger.debug("read_segy : Read segy data") # modified by A Squelch
return data, reel_header, trace_headers
def read_traces(f,
reel_header,
num_data,
bytes_per_sample,
index,
endian='>'): # added by A Squelch
"""Read the trace data.
values, SegyHeader, SegyTraceHeaders = read_traces(data,
reel_header,
num_data,
bytes_per_sample,
index)
"""
# Calculate number of dummy samples needed to account for Trace Headers
num_dummy_samples = TRACE_HEADER_NUM_BYTES / bytes_per_sample
logger.debug("read_traces : num_dummy_samples = " + str(num_dummy_samples))
# READ ALL SEGY TRACE HEADERS
trace_headers = read_all_trace_headers(f, reel_header)
logger.info("read_traces : Reading segy data")
dsf = reel_header['DataSampleFormat']
ctype = DATA_SAMPLE_FORMAT[dsf]
description = CTYPE_DESCRIPTION[ctype]
logger.debug("read_traces : Assuming DSF = {0}, {1}".format(
dsf, description))
values, _ = read_binary_value(f, index, ctype, endian, num_data)
logger.debug("read_traces : - reshaping")
values = reshape(values,
(reel_header['ntraces'],
reel_header['ns'] + num_dummy_samples))
logger.debug("read_traces : - stripping header dummy data")
values = values[:, num_dummy_samples:
(reel_header['ns'] + num_dummy_samples)]
logger.debug("read_traces : - transposing")
values = transpose(values)
# SOMEONE NEEDS TO IMPLEMENT A NICER WAY DO DEAL WITH DSF = 8
if reel_header['DataSampleFormat'] == 8:
for i in arange(reel_header['ntraces']):
for j in arange(reel_header['ns']):
if values[i][j] > 128:
values[i][j] = values[i][j] - 256
logger.debug("read_traces : Finished reading segy data")
return values, reel_header, trace_headers
def read_reel_header(f, endian='>'):
"""
reel_header = read_reel_header(file_handle)
"""
filename = _filename(f)
reel_header = {'filename': filename}
for key in HEADER_DEF.keys():
pos = HEADER_DEF[key]['pos']
format = HEADER_DEF[key]['type']
reel_header[key], index = read_binary_value(f, pos, format, endian)
logger.debug(str(pos) + " " +
str(format) +
" Reading " + key +
"=" + str(reel_header[key]))
# SET NUMBER OF BYTES PER DATA SAMPLE
bps = get_byte_per_sample(reel_header)
file_size = file_length(f)
ntraces = (file_size - REEL_HEADER_NUM_BYTES) / \
(reel_header['ns'] * bps + TRACE_HEADER_NUM_BYTES)
reel_header['ntraces'] = ntraces
logger.debug('read_reel_header : successfully read ' + filename)
return reel_header
def write_segy(filename, data, dt=1000, trace_header_in=None, header_in=None):
"""
write_segy(filename, data, dt)
Write SEGY
See also read_segy
(c) 2005, Thomas Mejer Hansen
MAKE OPTIONAL INPUT FOR ALL SEGYHTRACEHEADER VALUES
"""
if header_in is None:
header_in = {}
if trace_header_in is None:
trace_header_in = {}
logger.debug("write_segy : Trying to write " + filename)
shape = data.shape
ns = shape[0]
ntraces = shape[1]
print ntraces, ns
header = get_default_segy_header(ntraces, ns)
trace_header = get_default_segy_trace_headers(ntraces, ns, dt)
# Add trace_header_in, if exists...
for key in trace_header_in.keys():
print key
for a in range(ntraces):
trace_header[key] = trace_header_in[key][a]
# Add header_in, if exists...
for key in header_in.keys():
print key
header[key] = header_in[key]
write_segy_structure(filename, data, header, trace_header)
def write_segy_structure(filename,
data,
header,
trace_header,
endian='>'): # modified by A Squelch
"""
writeSegyStructure(filename, data, header, trace_header)
Write SEGY file using SegyPy data structures
See also readSegy
(c) 2005, Thomas Mejer Hansen
"""
logger.debug("writeSegyStructure : Trying to write " + filename)
f = open(filename, 'wb')
# VERBOSE INF
revision = canonicalize_revision(header['SegyFormatRevisionNumber'])
dsf = header['DataSampleFormat']
try: # block added by A Squelch
data_descriptor = HEADER_DEF['DataSampleFormat']['descr'][revision][dsf]
except KeyError:
logging.critical(" An error has occurred interpreting a SEGY binary"
"header key")
logging.critical(" Please check the Endian setting for this "
"file: {0}".format(header["filename"]))
sys.exit()
logger.debug("writeSegyStructure : SEG-Y revision = " + str(revision))
logger.debug("writeSegyStructure : DataSampleFormat = " +
str(dsf) +
"(" + data_descriptor + ")")
# WRITE SEGY HEADER
for key in HEADER_DEF.keys():
pos = HEADER_DEF[key]["pos"]
format = HEADER_DEF[key]["type"]
value = header[key]
put_value(value, f, pos, format, endian)
# SEGY TRACES
ctype = HEADER_DEF['DataSampleFormat']['datatype'][revision][dsf]
bps = HEADER_DEF['DataSampleFormat']['bps'][revision][dsf]
sizeT = TRACE_HEADER_NUM_BYTES + header['ns'] * bps
for itrace in range(header['ntraces']):
index = REEL_HEADER_NUM_BYTES + itrace * sizeT
logger.debug('Writing Trace #' +
str(itrace + 1) +
'/' + str(header['ntraces']))
# WRITE SEGY TRACE HEADER
for key in TRACE_HEADER_DEF.keys():
pos = index + TRACE_HEADER_DEF[key]['pos']
format = TRACE_HEADER_DEF[key]['type']
value = trace_header[key][itrace]
logger.debug(str(pos) + " " +
str(format) +
" Writing " + key +
"=" + str(value))
put_value(value, f, pos, format, endian)
# Write Data
cformat = endian + ctype
for s in range(header['ns']):
strVal = struct.pack(cformat, data[s, itrace])
f.seek(index +
TRACE_HEADER_NUM_BYTES +
s * struct.calcsize(cformat))
f.write(strVal)
f.close()
def put_value(value, fileid, index, ctype='l', endian='>', number=1):
"""
putValue(data, index, ctype, endian, number)
"""
ctype = CTYPES[ctype]
cformat = endian + ctype*number
logger.debug('putValue : cformat : ' + cformat + ' ctype = ' + ctype)
str_val = struct.pack(cformat, value)
fileid.seek(index)
fileid.write(str_val)
return 1
def create_binary_reader(f, ctype='l', endian='>'):
"""Create a unary callable which reads a given binary data type from a file.
"""
ctype = CTYPES[ctype]
size = size_in_bytes(ctype)
cformat = endian + ctype
def reader(index):
f.seek(index, os.SEEK_SET)
data = f.read(size)
# TODO: Check the content of data before proceeding
value = struct.unpack(cformat, data)
return value[0]
return reader
def read_binary_value(f, index, ctype='l', endian='>', number=1):
"""
read_binary_value(data, index, ctype, endian, number)
"""
ctype = CTYPES[ctype]
size = size_in_bytes(ctype)
cformat = endian + ctype * number
logger.debug('read_binary_value : cformat : ' + cformat)
index_end = index + size * number
f.seek(index, os.SEEK_SET)
data = f.read(size * number)
if ctype == 'ibm':
# ASSUME IBM FLOAT DATA
value = range(number)
for i in arange(number):
index_ibm = i * 4
value[i] = ibm2ieee2(data[index_ibm: index_ibm + 4])
# this returns an array as opposed to a tuple
else:
# TODO: Check the content of data before proceeding
value = struct.unpack(cformat, data)
if ctype == 'B':
logger.warning('read_binary_value : '
'Inefficient use of 1 byte Integer...', 1)
logger.debug('read_binary_value : ' +
'start = ' + str(index) +
' size = ' + str(size) +
' number = ' + str(number) +
' value = ' + str(value) +
' cformat = ' + str(cformat))
if number == 1:
return value[0], index_end
else:
return value, index_end
def get_byte_per_sample(header):
revision = canonicalize_revision(header["SegyFormatRevisionNumber"])
dsf = header["DataSampleFormat"]
try: # block added by A Squelch
bps = HEADER_DEF["DataSampleFormat"]["bps"][revision][dsf]
except KeyError:
# TODO: This should not be a critical failure - should just convert
# exception
logging.critical(" An error has occurred interpreting a SEGY "
"binary header key")
logging.critical("Please check the Endian setting for "
"this file: {0}".format(header["filename"]))
sys.exit()
logger.debug("getBytePerSample : bps = " + str(bps))
return bps
def main():
filename = r'C:\Users\rjs\opendtectroot\Blake_Ridge_Hydrates_3D' \
r'\stack_final_scaled50_int8.sgy'
with open(filename, 'rb') as segy:
data, header, trace_header = read_segy(segy)
if __name__ == '__main__':
main()
setup.cfg
+5
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@@ -0,0 +1,5 @@
[bdist_wheel]
# This flag says that the code is written to work on both Python 2 and Python
# 3. If at all possible, it is good practice to do this. If you cannot, you
# will need to generate wheels for each Python version that you support.
universal=1
setup.py
+119
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@@ -0,0 +1,119 @@
import io
import os
import re
from setuptools import setup, find_packages # Always prefer setuptools over distutils
from codecs import open # To use a consistent encoding
from os import path
def read(*names, **kwargs):
with io.open(
os.path.join(os.path.dirname(__file__), *names),
encoding=kwargs.get("encoding", "utf8")
) as fp:
return fp.read()
def find_version(*file_paths):
version_file = read(*file_paths)
version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
version_file, re.M)
if version_match:
return version_match.group(1)
raise RuntimeError("Unable to find version string.")
here = path.abspath(path.dirname(__file__))
# Get the long description from the relevant file
with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
long_description = f.read()
setup(
name='segpy',
# Versions should comply with PEP440. For a discussion on single-sourcing
# the version across setup.py and the project code, see
# https://packaging.python.org/en/latest/single_source_version.html
version=find_version("segpy/__init__.py"),
description='Transfer of seismic data to and from SEG Y files',
long_description=long_description,
# The project's main homepage.
url='https://github.com/rob-smallshire/segpy',
# Author details
author='Robert Smallshire',
author_email='robert@smallshire.org.uk',
# Choose your license
license='GPL',
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers=[
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 3 - Alpha',
# Indicate who your project is intended for
'Intended Audience :: Developers',
'Topic :: Scientific/Engineering',
'Topic :: Software Development :: Libraries',
# Pick your license as you wish (should match "license" above)
'License :: OSI Approved :: MIT License',
# Specify the Python versions you support here. In particular, ensure
# that you indicate whether you support Python 2, Python 3 or both.
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
],
# What does your project relate to?
keywords='seismic geocomputing geophysics',
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
packages=find_packages(exclude=['contrib', 'docs', 'test*']),
# List run-time dependencies here. These will be installed by pip when your
# project is installed. For an analysis of "install_requires" vs pip's
# requirements files see:
# https://packaging.python.org/en/latest/requirements.html
install_requires=[],
# List additional groups of dependencies here (e.g. development dependencies).
# You can install these using the following syntax, for example:
# $ pip install -e .[dev,test]
extras_require = {
'dev': ['check-manifest', 'wheel'],
'doc': ['sphinx', 'cartouche'],
'test': ['coverage', 'hypothesis'],
},
# If there are data files included in your packages that need to be
# installed, specify them here. If using Python 2.6 or less, then these
# have to be included in MANIFEST.in as well.
package_data={
},
# Although 'package_data' is the preferred approach, in some case you may
# need to place data files outside of your packages.
# see http://docs.python.org/3.4/distutils/setupscript.html#installing-additional-files
# In this case, 'data_file' will be installed into '<sys.prefix>/my_data'
data_files=[],
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
entry_points={
'console_scripts': [
],
},
)
test/__init__.py
+1
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@@ -0,0 +1 @@
test/strategies.py
+21
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@@ -0,0 +1,21 @@
from hypothesis import strategy
from hypothesis.specifiers import integers_in_range
PRINTABLE_ASCII_RANGE = (32, 127)
def multiline_ascii_encodable_text(min_num_lines, max_num_lines):
"""A Hypothesis strategy to produce a multiline Unicode string.
Args:
min_num_lines: The minimum number of lines in the produced strings.
max_num_lines: The maximum number of lines in the produced strings.
Returns:
A strategy for generating Unicode strings containing only newlines
and characters which are encodable as printable 7-bit ASCII characters.
"""
return strategy(integers_in_range(0, 10)) \
.flatmap(lambda n: ([integers_in_range(*PRINTABLE_ASCII_RANGE)],) * n) \
.map(lambda xs: '\n'.join(bytes(x).decode('ascii') for x in xs))
test/test-requirements.txt
+1
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@@ -0,0 +1 @@
hypothesis>=1.2
test/test_extended_textual_header.py
+41
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@@ -0,0 +1,41 @@
import unittest
from hypothesis import given
from hypothesis.specifiers import sampled_from, just
from segpy.encoding import EBCDIC, ASCII
from segpy.toolkit import format_extended_textual_header, CARDS_PER_HEADER, END_TEXT_STANZA, CARD_LENGTH
from test.strategies import multiline_ascii_encodable_text
class TestFormatExtendedTextualHeader(unittest.TestCase):
@given(multiline_ascii_encodable_text(0, 100),
sampled_from([ASCII, EBCDIC]),
bool)
def test_forty_lines_per_page(self, text, encoding, include_text_stop):
pages = format_extended_textual_header(text, encoding, include_text_stop)
self.assertTrue(all(len(page) == CARDS_PER_HEADER for page in pages))
@given(multiline_ascii_encodable_text(0, 100),
sampled_from([ASCII, EBCDIC]),
bool)
def test_eighty_bytes_per_encoded_line(self, text, encoding, include_text_stop):
pages = format_extended_textual_header(text, encoding, include_text_stop)
self.assertTrue(all([len(line.encode(encoding)) == CARD_LENGTH for page in pages for line in page]))
@given(multiline_ascii_encodable_text(0, 100),
sampled_from([ASCII, EBCDIC]),
bool)
def test_lines_end_with_cr_lf(self, text, encoding, include_text_stop):
pages = format_extended_textual_header(text, encoding, include_text_stop)
self.assertTrue(all([line.endswith('\r\n') for page in pages for line in page]))
@given(multiline_ascii_encodable_text(0, 100),
sampled_from([ASCII, EBCDIC]),
just(True))
def test_end_text_stanza_present(self, text, encoding, include_text_stop):
pages = format_extended_textual_header(text, encoding, include_text_stop)
self.assertTrue(pages[-1][0].startswith(END_TEXT_STANZA))
if __name__ == '__main__':
unittest.main()
test/test_float.py
+364
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from math import trunc, floor
import unittest
from hypothesis import given, assume
import math
from hypothesis.specifiers import integers_in_range, floats_in_range
from segpy.portability import byte_string
from segpy.ibm_float import (ieee2ibm, ibm2ieee, MAX_IBM_FLOAT, SMALLEST_POSITIVE_NORMAL_IBM_FLOAT,
LARGEST_NEGATIVE_NORMAL_IBM_FLOAT, MIN_IBM_FLOAT, IBMFloat, EPSILON_IBM_FLOAT,
MAX_EXACT_INTEGER_IBM_FLOAT, MIN_EXACT_INTEGER_IBM_FLOAT, EXPONENT_BIAS)
from segpy.util import almost_equal
class Ibm2Ieee(unittest.TestCase):
def test_zero(self):
self.assertEqual(ibm2ieee(b'\0\0\0\0'), 0.0)
def test_positive_half(self):
self.assertEqual(ibm2ieee(byte_string((0b11000000, 0x80, 0x00, 0x00))), -0.5)
def test_negative_half(self):
self.assertEqual(ibm2ieee(byte_string((0b01000000, 0x80, 0x00, 0x00))), 0.5)
def test_one(self):
self.assertEqual(ibm2ieee(b'\x41\x10\x00\x00'), 1.0)
def test_negative_118_625(self):
# Example taken from Wikipedia http://en.wikipedia.org/wiki/IBM_Floating_Point_Architecture
self.assertEqual(ibm2ieee(byte_string((0b11000010, 0b01110110, 0b10100000, 0b00000000))), -118.625)
def test_largest_representable_number(self):
self.assertEqual(ibm2ieee(byte_string((0b01111111, 0b11111111, 0b11111111, 0b11111111))), MAX_IBM_FLOAT)
def test_smallest_positive_normalised_number(self):
self.assertEqual(ibm2ieee(byte_string((0b00000000, 0b00010000, 0b00000000, 0b00000000))), SMALLEST_POSITIVE_NORMAL_IBM_FLOAT)
def test_largest_negative_normalised_number(self):
self.assertEqual(ibm2ieee(byte_string((0b10000000, 0b00010000, 0b00000000, 0b00000000))), LARGEST_NEGATIVE_NORMAL_IBM_FLOAT)
def test_smallest_representable_number(self):
self.assertEqual(ibm2ieee(byte_string((0b11111111, 0b11111111, 0b11111111, 0b11111111))), MIN_IBM_FLOAT)
def test_error_1(self):
self.assertEqual(ibm2ieee(byte_string((196, 74, 194, 143))), -19138.55859375)
def test_error_2(self):
self.assertEqual(ibm2ieee(byte_string((191, 128, 0, 0))), -0.03125)
def test_subnormal(self):
self.assertEqual(ibm2ieee(byte_string((0x00, 0x00, 0x00, 0x20))), 1.6472184286297693e-83)
def test_subnormal_is_subnormal(self):
self.assertTrue(0 < ibm2ieee(byte_string((0x00, 0x00, 0x00, 0x20))) < SMALLEST_POSITIVE_NORMAL_IBM_FLOAT)
def test_subnormal_smallest_subnormal(self):
self.assertEqual(ibm2ieee(byte_string((0x00, 0x00, 0x00, 0x01))), 5.147557589468029e-85)
class Ieee2Ibm(unittest.TestCase):
def test_zero(self):
self.assertEqual(ieee2ibm(0.0), b'\0\0\0\0')
def test_positive_half(self):
self.assertEqual(ieee2ibm(-0.5), byte_string((0b11000000, 0x80, 0x00, 0x00)))
def test_negative_half(self):
self.assertEqual(ieee2ibm(0.5), byte_string((0b01000000, 0x80, 0x00, 0x00)))
def test_one(self):
self.assertEqual(ieee2ibm(1.0), b'\x41\x10\x00\x00')
def test_negative_118_625(self):
# Example taken from Wikipedia http://en.wikipedia.org/wiki/IBM_Floating_Point_Architecture
self.assertEqual(ieee2ibm(-118.625), byte_string((0b11000010, 0b01110110, 0b10100000, 0b00000000)))
def test_0_1(self):
# Note, this is different from the Wikipedia example, because the Wikipedia example does
# round to nearest, and our routine does round to zero
self.assertEqual(ieee2ibm(0.1), byte_string((0b01000000, 0b00011001, 0b10011001, 0b10011001)))
def test_subnormal(self):
self.assertEqual(ieee2ibm(1.6472184286297693e-83), byte_string((0x00, 0x00, 0x00, 0x20)))
def test_smallest_subnormal(self):
self.assertEqual(ieee2ibm(5.147557589468029e-85), byte_string((0x00, 0x00, 0x00, 0x01)))
def test_too_small_subnormal(self):
with self.assertRaises(FloatingPointError):
ieee2ibm(1e-86)
def test_nan(self):
with self.assertRaises(ValueError):
ieee2ibm(float('nan'))
def test_inf(self):
with self.assertRaises(ValueError):
ieee2ibm(float('inf'))
def test_too_large(self):
with self.assertRaises(OverflowError):
ieee2ibm(MAX_IBM_FLOAT * 10)
def test_too_small(self):
with self.assertRaises(OverflowError):
ieee2ibm(MIN_IBM_FLOAT * 10)
class Ibm2IeeeRoundtrip(unittest.TestCase):
def test_zero(self):
ibm_start = b'\0\0\0\0'
f = ibm2ieee(ibm_start)
ibm_result = ieee2ibm(f)
self.assertEqual(ibm_start, ibm_result)
def test_positive_half(self):
ibm_start = byte_string((0b11000000, 0x80, 0x00, 0x00))
f = ibm2ieee(ibm_start)
ibm_result = ieee2ibm(f)
self.assertEqual(ibm_start, ibm_result)
def test_negative_half(self):
ibm_start = byte_string((0b01000000, 0x80, 0x00, 0x00))
f = ibm2ieee(ibm_start)
ibm_result = ieee2ibm(f)
self.assertEqual(ibm_start, ibm_result)
def test_one(self):
ibm_start = b'\x41\x10\x00\x00'
f = ibm2ieee(ibm_start)
ibm_result = ieee2ibm(f)
self.assertEqual(ibm_start, ibm_result)
def test_subnormal(self):
ibm_start = byte_string((0x00, 0x00, 0x00, 0x20))
f = ibm2ieee(ibm_start)
ibm_result = ieee2ibm(f)
self.assertEqual(ibm_start, ibm_result)
class TestIBMFloat(unittest.TestCase):
def test_zero_from_float(self):
zero = IBMFloat.from_float(0.0)
self.assertTrue(zero.is_zero())
def test_zero_from_bytes(self):
zero = IBMFloat.from_bytes(b'\x00\x00\x00\x00')
self.assertTrue(zero.is_zero())
def test_subnormal(self):
ibm = IBMFloat.from_float(1.6472184286297693e-83)
self.assertTrue(ibm.is_subnormal())
def test_smallest_subnormal(self):
ibm = IBMFloat.from_float(5.147557589468029e-85)
self.assertEqual(bytes(ibm), byte_string((0x00, 0x00, 0x00, 0x01)))
def test_too_small_subnormal(self):
with self.assertRaises(FloatingPointError):
IBMFloat.from_float(1e-86)
def test_nan(self):
with self.assertRaises(ValueError):
IBMFloat.from_float(float('nan'))
def test_inf(self):
with self.assertRaises(ValueError):
IBMFloat.from_float(float('inf'))
def test_too_large(self):
with self.assertRaises(OverflowError):
IBMFloat.from_float(MAX_IBM_FLOAT * 10)
def test_too_small(self):
with self.assertRaises(OverflowError):
IBMFloat.from_float(MIN_IBM_FLOAT * 10)
@given(floats_in_range(MIN_IBM_FLOAT, MAX_IBM_FLOAT))
def test_bool(self, f):
self.assertEqual(bool(IBMFloat.from_float(f)), bool(f))
@given(integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(0, 255))
def test_bytes_roundtrip(self, a, b, c, d):
b = byte_string((a, b, c, d))
ibm = IBMFloat.from_bytes(b)
self.assertEqual(bytes(ibm), b)
@given(floats_in_range(MIN_IBM_FLOAT, MAX_IBM_FLOAT))
def test_floats_roundtrip(self, f):
ibm = IBMFloat.from_float(f)
self.assertTrue(almost_equal(f, float(ibm), epsilon=EPSILON_IBM_FLOAT))
@given(integers_in_range(0, MAX_EXACT_INTEGER_IBM_FLOAT - 1),
floats_in_range(0.0, 1.0))
def test_trunc_above_zero(self, i, f):
assume(f != 1.0)
ieee = i + f
ibm = IBMFloat.from_float(ieee)
self.assertEqual(trunc(ibm), i)
@given(integers_in_range(MIN_EXACT_INTEGER_IBM_FLOAT + 1, 0),
floats_in_range(0.0, 1.0))
def test_trunc_below_zero(self, i, f):
assume(f != 1.0)
ieee = i - f
ibm = IBMFloat.from_float(ieee)
self.assertEqual(trunc(ibm), i)
@given(integers_in_range(MIN_EXACT_INTEGER_IBM_FLOAT, MAX_EXACT_INTEGER_IBM_FLOAT - 1),
floats_in_range(0.0, 1.0))
def test_ceil(self, i, f):
assume(f != 1.0)
ieee = i + f
ibm = IBMFloat.from_float(ieee)
self.assertEqual(math.ceil(ibm), i + 1)
@given(integers_in_range(MIN_EXACT_INTEGER_IBM_FLOAT, MAX_EXACT_INTEGER_IBM_FLOAT - 1),
floats_in_range(0.0, 1.0))
def test_floor(self, i, f):
assume(f != 1.0)
ieee = i + f
ibm = IBMFloat.from_float(ieee)
self.assertEqual(math.floor(ibm), i)
def test_normalise_subnormal_expect_failure(self):
# This float has an base-16 exponent of -64 (the minimum) and cannot be normalised
ibm = IBMFloat.from_float(1.6472184286297693e-83)
assert ibm.is_subnormal()
with self.assertRaises(FloatingPointError):
ibm.normalize()
def test_normalise_subnormal1(self):
ibm = IBMFloat.from_bytes((0b01000000, 0b00000000, 0b11111111, 0b00000000))
assert ibm.is_subnormal()
normalized = ibm.normalize()
self.assertFalse(normalized.is_subnormal())
def test_normalise_subnormal2(self):
ibm = IBMFloat.from_bytes((64, 1, 0, 0))
assert ibm.is_subnormal()
normalized = ibm.normalize()
self.assertFalse(normalized.is_subnormal())
@given(integers_in_range(128, 255),
integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(4, 23))
def test_normalise_subnormal(self, b, c, d, shift):
mantissa = (b << 16) | (c << 8) | d
assume(mantissa != 0)
mantissa >>= shift
assert mantissa != 0
sa = EXPONENT_BIAS
sb = (mantissa >> 16) & 0xff
sc = (mantissa >> 8) & 0xff
sd = mantissa & 0xff
ibm = IBMFloat.from_bytes((sa, sb, sc, sd))
assert ibm.is_subnormal()
normalized = ibm.normalize()
self.assertFalse(normalized.is_subnormal())
@given(integers_in_range(128, 255),
integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(4, 23))
def test_zero_subnormal(self, b, c, d, shift):
mantissa = (b << 16) | (c << 8) | d
assume(mantissa != 0)
mantissa >>= shift
assert mantissa != 0
sa = EXPONENT_BIAS
sb = (mantissa >> 16) & 0xff
sc = (mantissa >> 8) & 0xff
sd = mantissa & 0xff
ibm = IBMFloat.from_bytes((sa, sb, sc, sd))
assert ibm.is_subnormal()
z = ibm.zero_subnormal()
self.assertTrue(z.is_zero())
@given(integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(0, 255))
def test_abs(self, a, b, c, d):
ibm = IBMFloat.from_bytes((a, b, c, d))
abs_ibm = abs(ibm)
self.assertGreaterEqual(abs_ibm.signbit, 0)
@given(integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(0, 255),
integers_in_range(0, 255))
def test_negate_non_zero(self, a, b, c, d):
ibm = IBMFloat.from_bytes((a, b, c, d))
assume(not ibm.is_zero())
negated = -ibm
self.assertNotEqual(ibm.signbit, negated.signbit)
def test_negate_zero(self):
zero = IBMFloat.from_float(0.0)
negated = -zero
self.assertTrue(negated.is_zero())
@given(floats_in_range(MIN_IBM_FLOAT, MAX_IBM_FLOAT))
def test_signbit(self, f):
ltz = f < 0
ibm = IBMFloat.from_float(f)
self.assertEqual(ltz, ibm.signbit)
@given(floats_in_range(-1.0, +1.0),
integers_in_range(-256, 255))
def test_ldexp_frexp(self, fraction, exponent):
try:
ibm = IBMFloat.ldexp(fraction, exponent)
except OverflowError:
assume(False)
else:
f, e = ibm.frexp()
self.assertTrue(almost_equal(fraction * 2**exponent, f * 2**e, epsilon=EPSILON_IBM_FLOAT))
@given(floats_in_range(MIN_IBM_FLOAT, MAX_IBM_FLOAT),
floats_in_range(0.0, 1.0))
def test_add(self, f, p):
a = f * p
b = f - a
ibm_a = IBMFloat.from_float(a)
ibm_b = IBMFloat.from_float(b)
ibm_c = ibm_a + ibm_b
ieee_a = float(ibm_a)
ieee_b = float(ibm_b)
ieee_c = ieee_a + ieee_b
self.assertTrue(almost_equal(ieee_c, ibm_c, epsilon=EPSILON_IBM_FLOAT * 4))
@given(floats_in_range(0, MAX_IBM_FLOAT),
floats_in_range(0, MAX_IBM_FLOAT))
def test_sub(self, a, b):
ibm_a = IBMFloat.from_float(a)
ibm_b = IBMFloat.from_float(b)
ibm_c = ibm_a - ibm_b
ieee_a = float(ibm_a)
ieee_b = float(ibm_b)
ieee_c = ieee_a - ieee_b
self.assertTrue(almost_equal(ieee_c, ibm_c, epsilon=EPSILON_IBM_FLOAT))
if __name__ == '__main__':
unittest.main()
test/test_util.py
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import unittest
from hypothesis import given, assume
from hypothesis.descriptors import integers_in_range
from segpy.util import batched
class TestBatched(unittest.TestCase):
@given([int],
integers_in_range(1, 1000))
def test_batch_sizes_unpadded(self, items, batch_size):
assume(batch_size > 0)
batches = list(batched(items, batch_size))
self.assertTrue(all(len(batch) == batch_size for batch in batches[:-1]))
@given([int],
integers_in_range(1, 1000))
def test_final_batch_sizes(self, items, batch_size):
assume(len(items) > 0)
assume(batch_size > 0)
batches = list(batched(items, batch_size))
self.assertTrue(len(batches[-1]) <= batch_size)
@given([int],
integers_in_range(1, 1000),
int)
def test_batch_sizes_padded(self, items, batch_size, pad):
assume(batch_size > 0)
batches = list(batched(items, batch_size, padding=pad))
self.assertTrue(all(len(batch) == batch_size for batch in batches))
@given([int],
integers_in_range(1, 1000),
int)
def test_pad_contents(self, items, batch_size, pad):
assume(len(items) > 0)
assume(0 < batch_size < 1000)
num_left_over = len(items) % batch_size
pad_length = batch_size - num_left_over if num_left_over != 0 else 0
assume(pad_length != 0)
batches = list(batched(items, batch_size, padding=pad))
self.assertEqual(batches[-1][batch_size - pad_length:], [pad] * pad_length)
def test_pad(self):
batches = list(batched([0, 0], 3, 42))
self.assertEqual(batches[-1], [0, 0, 42])
if __name__ == '__main__':
unittest.main()
testsegy.py
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@@ -1,80 +0,0 @@
#!/usr/bin/env python
#
# testsegy.py
#
import segypy
def test_read(filename):
# Read Segy File
with open(filename, 'rb') as f:
return segypy.read_segy(f, filename)
def test_write(filename_out, data, sh, sth):
sh['DataSampleFormat'] = 5
sh['SegyFormatRevisionNumber'] = 100
segypy.write_segy_structure(filename_out, data, sh, sth)
segypy.wiggle(data, sh, 2, .1, .1)
f_ieee = 'data_IEEE.segy'
f_ibm = 'data_IBM_REV1.segy'
d_ieee, sh, sth = segypy.read_segy(f_ieee)
d_ibm, sh, sth = segypy.read_segy(f_ibm)
return d_ieee, d_ibm, data
def test_render(d_ieee, d_ibm, data):
import pylab
# imshow(Data)
pylab.figure(1)
pylab.imshow(d_ieee)
pylab.title('ieee')
pylab.show()
pylab.figure(2)
pylab.imshow(d_ibm)
pylab.title('IBM')
pylab.show()
pylab.figure(3)
pylab.imshow(data)
pylab.title('TEST')
pylab.show()
def parse_args():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('filename',
help='The SEGY input file')
parser.add_argument('--output', '-o',
dest='outfile',
default='',
help='The output file (optional).')
parser.add_argument('--render_test', '-r',
dest='render_test',
action='store_true',
help='Whether to test rendering (only applies if '
'output is produced.)')
return parser.parse_args()
if __name__ == '__main__':
args = parse_args()
read_results = test_read(args.filename)
if args.outfile:
write_results = test_write(args.outfile, *read_results)
if args.render_test:
test_render(*write_results)