Merge coverage states into main .css.

TASKS.txt

@@ -19,6 +19,8 @@ Tasks
 
 :doc:`gsoc2011`
 
+:doc:`coverage_table`
+
 Infrastructure
 --------------
 - :strike:`Implement a new backend system so that we may start including

doc/source/_static/default.css_t

@@ -273,3 +273,51 @@ th {
   font-size: 80%;
 }
 
+/* Coverage States */
+span.missing{
+	color: #000;
+	background-color: #ff5840;
+	border-color: #A77272;
+	font-weight: bold;
+}
+span.partial{
+	color: #806600;
+	background-color: #ffc343;
+	font-weight: bold;
+}
+span.done{
+	color: #106600;
+	background-color: #60f030;
+	border-color: #4F8530;
+	font-weight: bold;
+}
+span.na{
+	color: #A8A8A8;
+	border-color: #4F8530;
+}
+span.missing-bar{
+	color: #000;
+	background-color: #ff5840;
+	border-color: #A77272;
+	font-weight: normal;
+	font-style: normal;
+}
+span.partial-bar{
+	color: #806600;
+	background-color: #ffc343;
+	font-weight: normal;
+	font-style: normal;
+}
+span.done-bar{
+	color: #106600;
+	background-color: #60f030;
+	border-color: #4F8530;
+	font-weight: normal;
+	font-style: normal;
+}
+span.na-bar{
+	color: #A8A8A8;
+	border-color: #4F8530;
+	font-weight: normal;
+	font-style: normal;
+}

doc/source/coverage.csv

@@ -0,0 +1 @@
+Image Display and Exploration,Image Display and Exploration,Image File I/O,Image Types and Type Conversions
GUI Tools,Modular Interactive Tools,Navigational Tools for Image Scroll Panel,Utilities for Interactive Tools
Spatial Transformations and Image Registration,Spatial Transformations,Image Registration,
Image Analysis and Statistics,Image Analysis,Texture Analysis,Pixel Values and Statistics
Image Arithmetic,,,
Image Enhancement and Restoration,Image Enhancement,Image Restoration (Deblurring),
Linear Filtering and Transforms,Linear Filtering,Linear 2-D Filter Design,Image Transforms
Morphological Operations,Intensity and Binary Images,Binary Images,Structuring Element Creation and Manipulation
"ROI-Based, Neighborhood, and Block Processing",ROI-Based Processing,Neighborhood and Block Processing,
Colormaps and Color Space,Color Space Conversions,,
Utilities,Validation,Array Operations,Performance
,,,
Make movie from multiframe image                    ,immovie ,:done:`immovie`,:partial:`immovie`
"Play movies, videos, or image sequences           ",implay  ,:na:`n/a`,
Display image                                       ,imshow  ,,
Image Tool                                          ,imtool  ,,
Display multiple image frames as rectangular montage,montage ,,
Display multiple images in single figure            ,subimage,,
Display image as texture-mapped surface             ,warp    ,,
,                                                                  ,,
Read metadata from header file of Analyze 7.5 data set             ,analyze75info,,
Read image data from image file of Analyze 7.5 data set            ,analyze75read,,
Anonymize DICOM file                                               ,dicomanon    ,,
Get or set active DICOM data dictionary                            ,dicomdict    ,,
Read metadata from DICOM message                                   ,dicominfo    ,,
Find attribute in DICOM data dictionary                            ,dicomlookup  ,,
Read DICOM image                                                   ,dicomread    ,,
Generate DICOM unique identifier                                   ,dicomuid     ,,
Write images as DICOM files                                        ,dicomwrite   ,,
Read high dynamic range (HDR) image                                ,hdrread      ,,
Write Radiance high dynamic range (HDR) image file                 ,hdrwrite     ,,
Read metadata from Interfile file                                  ,interfileinfo,,
Read images in Interfile format                                    ,interfileread,,
Check if file is R-Set                                             ,isrset       ,,
Create high dynamic range image                                    ,makehdr      ,,
Read metadata from National Imagery Transmission Format (NITF) file,nitfinfo     ,,
Read image from NITF file                                          ,nitfread     ,,
Open R-Set file                                                    ,openrset     ,,
Create reduced resolution data set from image file                 ,rsetwrite    ,,
Render high dynamic range image for viewing                        ,tonemap      ,,
,,,
Convert Bayer pattern encoded image to truecolor image,demosaic,,
Convert grayscale or binary image to indexed image,gray2ind,,
Convert grayscale image to indexed image using multilevel thresholding,grayslice,,
Global image threshold using Otsu's method,graythresh,,
"Convert image to binary image, based on threshold",im2bw,,
Convert image to double precision,im2double,,
Convert image to 16-bit signed integers,im2int16,,
Convert image to Java buffered image,im2java2d,,
Convert image to single precision,im2single,,
Convert image to 16-bit unsigned integers,im2uint16,,
Convert image to 8-bit unsigned integers,im2uint8,,
Convert indexed image to grayscale image,ind2gray,,
Convert indexed image to RGB image,ind2rgb,,
Convert label matrix into RGB image,label2rgb,,
Convert matrix to grayscale image,mat2gray,,
Convert RGB image or colormap to grayscale,rgb2gray,,
,,,
Image Information tool,imageinfo,,
Adjust Contrast tool,imcontrast,,
Display Range tool,imdisplayrange,,
Distance tool,imdistline,,
Pixel Information tool,impixelinfo,,
Pixel Information tool without text label,impixelinfoval,,
Pixel Region tool,impixelregion,,
Pixel Region tool panel,impixelregionpanel,,
,,,
Magnification box for scroll panel,immagbox,,
Overview tool for image displayed in scroll panel,imoverview,,
Overview tool panel for image displayed in scroll panel,imoverviewpanel,,
Scroll panel for interactive image navigation,imscrollpanel,,
,,,
Convert axes coordinates to pixel coordinates,axes2pix,,
Image data from axes,getimage,,
Image model object from image object,getimagemodel,,
Information about image attributes,imattributes,,
Create draggable ellipse,imellipse,,
Create draggable freehand region,imfreehand,,
Get handle to current axes containing image,imgca,,
Get handle to current figure containing image,imgcf,,
Open Image dialog box,imLine truncated

doc/source/coverage_generator.py

@@ -0,0 +1,262 @@
+#!/usr/bin/env python
+
+import sys
+import os
+import csv
+
+# Import StringIO module
+try:
+    import cStringIO as StringIO
+except ImportError:
+    import StringIO
+
+# Missing item value
+MISSING_STRING=":missing:`Not Implemented`"
+
+def calculate_coverage(reader,blocks=100):
+    r"""Calculate portions of code that are in one of the coverage categories
+    
+    Returns a tuple representing the weighted items as integers.  The order is
+        
+        (done,partial,missing,not applicable)
+    """
+    # Coverage counters
+    total_items = 0
+    partial_items = 0
+    done_items = 0
+    na_items = 0
+
+    # Skip table names
+    for row in reader:
+        if len(row[0]) == 0:
+            break
+
+    # Count items
+    for row in reader:
+        if len(row[0]) > 0:
+            total_items += 1
+            if ":done:" in row[2] or ":done:" in row[3]:
+                done_items += 1
+            elif ":partial:" in row[2] or ":partial:" in row[3]:
+                partial_items += 1
+            elif ":na:" in row[2] or ":na:" in row[3]:
+                na_items += 1
+    
+    weight = float(blocks) / total_items
+    
+    return (int(weight*done_items),
+            int(weight*partial_items),
+            int(weight*(total_items - (partial_items + done_items + na_items))),
+            int(weight*na_items))
+                
+
+def read_table_titles(reader):
+    r"""Create a dictionary with keys as section names and values as a list of
+    table names
+    
+    return (dict)
+    """
+    section_titles = []
+    table_names = {}
+    try:
+        for row in reader:
+            names = []
+            # End of names table
+            if len(row[0]) == 0:
+                break
+            # Extract names of the tables
+            for name in row[1:]:
+                if len(name) > 0:
+                    names.append(name) 
+                else:
+                    break
+            section_titles.append(row[0])
+            table_names[row[0]] = names
+    except csv.Error, e:
+        sys.exit('line %d: %s' % (reader.line_num, e))
+    
+    return section_titles,table_names
+
+def table_seperator(stream,lengths,character="-"):
+    r"""Write out table row seperator
+    
+    :Input:
+     - *stream* (io/stream) Stream where output is put
+     - *lengths* (list) A list of the lengths of the columns
+     - *character* (string) Character to be filled between +, defaults to "-".
+     
+    """
+    stream.write("+")
+    stream.write('+'.join([character*(length+2) for length in lengths]))
+    stream.write("+")
+    
+def table_row(stream,data,lengths,num_columns=None):
+    r"""Write out table row data
+    
+    :Input:
+     - *stream* (io/stream) Stream where output is put
+     - *data* (list) List of strings containing data
+     - *lengths* (list) A list of the lengths of the columns
+     - *num_columns* (string) Number of columns, defaults to the length of the 
+       data array
+     
+    """
+    if num_columns is None:
+        num_columns = len(data)
+    stream.write("|")
+    for i in xrange(num_columns):
+        if len(data)-1 >= i:
+            if len(data[i]) == 0:
+                entry = MISSING_STRING
+            else:
+                entry = data[i]
+        else:
+            entry = MISSING_STRING
+        stream.write(" " + entry + " "*(lengths[i] - len(entry)) + " |")
+    
+def generate_table(reader,stream,table_name=None,
+                    column_titles=["Functionality","Matlab","Scipy","Scipy"]):
+    r"""Generate a reST grid table based on the CSV data in reader
+    
+    Reads CSV data from *reader* until an empty line is found and generates a
+    reST table based on the data into *stream*.  A table name can be given for
+    a section and table label.  All rows are read in and checked for maximum
+    number of columns (defaults to the size of column_titles) and column
+    widths so that the table can be constructed.  If a row contains less than
+    the maximum number of columns a string is inserted that defaults to the
+    string *MISSING_STRING* which is a global parameter.
+    
+    :Input:
+     - reader (csv.reader) The CSV reader to read in from
+     - stream (iostream) Output target
+     - table_name (string) Optional name of table, defaults to *None*
+     - column_titles (list) List of column titles
+     
+    """
+    # Find number of columns and column widths, base number of columns is
+    # determined by the headers
+    num_columns = len(column_titles)
+    data = [column_titles]
+    try:
+        for row in reader:
+            # print row
+            if len(row[0]) == 0:
+                break
+            data.append([entry.expandtabs() for entry in row])
+            num_columns = max(num_columns,len(row))
+    except csv.Error, e:
+        sys.exit('line %d: %s' % (reader.line_num, e))
+
+    column_lengths = [len(MISSING_STRING)]*num_columns
+    for row in data:
+        for i in xrange(len(row)):
+            column_lengths[i] = max(column_lengths[i],len(row[i]))
+    
+    # Output table header
+    stream.write(table_name + "\n")
+    if table_name is not None:
+        stream.write("~"*len(table_name)+"\n\n")
+    stream.write(".. tabularcolumns:: |p{40%}|p{20%}|p{20%}|p{20%}|\n\n")
+    if table_name is not None:
+        stream.write(".. table::%s\n\n" % table_name)
+    table_seperator(stream,column_lengths,character="-")
+    stream.write("\n")
+    table_row(stream,data[0],column_lengths,num_columns)
+    stream.write("\n")
+    table_seperator(stream,column_lengths,character="=")
+    stream.write("\n")
+    
+    # Output table data
+    for row in data[1:]:
+        table_row(stream,row,column_lengths,num_columns)
+        stream.write("\n")
+        table_seperator(stream,column_lengths,character='-')
+        stream.write("\n")
+    stream.write("\n\n")
+    
+def generate_page(csv_path,stream,page_title="Coverage Tables"):
+    r"""Generate coverage table page
+    
+    Generates all reST for all tables contained in the CSV file at *csv_path*
+    and output it to *stream*.
+    
+    :Input:
+     - *csv_path* (path) Path to CSV file
+     - *stream* (iostream) Output stream
+     - *page_title* (string) Optional page title, defaults to 
+       ``Coverage Tables``.
+    """
+    # Open reader
+    csv_file = open(csv_path,'U')
+    
+    # Sniffer does not seem to work all the time even when an Excel
+    # spread sheet is being used
+    # dialect = csv.Sniffer().sniff(csv_file.read(1024))
+    # csv_file.seek(0)
+    # reader = csv.reader(csv_file, dialect)
+    
+    reader = csv.reader(csv_file)
+    item_counts = calculate_coverage(reader,blocks=90)
+    csv_file.seek(0)
+    
+    # Write out header
+    stream.write("%s\n" % page_title)
+    stream.write("="*len(page_title) + "\n\n")
+    stream.write(".. role:: missing\n")
+    stream.write(".. role:: partial\n")
+    stream.write(".. role:: done\n")
+    stream.write(".. role:: na\n\n")
+    stream.write(".. role:: missing-bar\n")
+    stream.write(".. role:: partial-bar\n")
+    stream.write(".. role:: done-bar\n")
+    stream.write(".. role:: na-bar\n\n")
+    stream.write("Color Key\n")
+    stream.write("---------\n")
+    stream.write(":done:`Complete` ")
+    stream.write(":partial:`Partial` ")
+    stream.write(":missing:`Missing` ")
+    stream.write(":na:`Not applicable`\n\n")
+    stream.write("Coverage Bar\n")
+    stream.write("------------\n\n")
+    if item_counts[0] > 0:
+        stream.write(":done-bar:`%s` " % ("="*item_counts[0]))
+    if item_counts[1] > 0:
+        stream.write(":partial-bar:`%s` " % ("="*item_counts[1]))
+    if item_counts[2] > 0:
+        stream.write(":missing-bar:`%s` " % ("="*item_counts[2]))
+    if item_counts[3] > 0:
+        stream.write(":na-bar:`%s`" % ("="*item_counts[3]))
+    stream.write("\n\n")
+    
+    sections,table_names = read_table_titles(reader)
+    for section_name in sections:
+        stream.write(section_name + "\n")
+        stream.write("-"*len(section_name) + "\n\n")
+        for table_name in table_names[section_name]:
+            generate_table(reader,stream,table_name)
+    
+    csv_file.close()
+
+if __name__ == "__main__":
+    csv_path = './coverage.csv'
+    output_path = './coverage_table.txt'
+    if len(sys.argv) > 1:
+        if sys.argv[1][:5].lower() == "help":
+            print "Coverage Table Generator: coverage_generator.py"
+            print "  Usage: coverage_generator.py [csv] [output]"
+            print "    csv - Path to csv file, defaults to ./coverage.csv"
+            print "    output - Ouput path, defaults to ./coverage_table.txt"
+            print ""
+            sys.exit(0)
+        if len(sys.argv) == 2:
+            csv_path = os.path.abspath(sys.argv[1])
+        if len(sys.argv) == 3:
+            output_path = os.path.abspath(sys.argv[2])
+    
+    output = open(output_path,'w')
+    generate_page(csv_path,output)
+    output.close()
+    
+    print "Generated %s from %s." % (output_path,csv_path)
+
+