mirror of
https://github.com/wassname/mammoviews.git
synced 2026-06-27 16:10:25 +08:00
Dmytro S Lituiev
98 lines
4.4 KiB
Python
98 lines
4.4 KiB
Python
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# coding: utf-8
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#cell#
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import pandas as pd
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import sys
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from header_cleaner import get_features, normalize_fields, parse_float_tuples, parse_float
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#cell#
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fn_features = "../tables/df_all_mammos_dicom_headers_selected.tab.gz"
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outfn = "../tables/df_all_mammos_dicom_headers_selected_norm.tab"
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dffeatures = pd.read_table(fn_features, index_col="filename")
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#cell#
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mask_nonnumeric = ~dffeatures["ContentTime"].map(lambda x: isinstance(x, float) | isinstance(x, int))
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dffeatures.loc[mask_nonnumeric, "ContentTime"] = dffeatures["ContentTime"][mask_nonnumeric].map(lambda x: float(x.replace(':','').replace('--',"30")))
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#cell#
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print("shape", dffeatures.shape)
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#cell#
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normalize_fun = {"0_ViewCodeSequence__0_ViewModifierCodeSequence_CodeMeaning":
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lambda x: str(x).lower(),
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"0_ViewCodeSequence_CodeValue": lambda x: str(x),
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"Grid": lambda x: str(x).replace("'","")
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.replace("(","").replace(")","")
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.replace(",","").replace("/"," ")
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.replace('PARRALLEL',"PARALLEL")
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.lower(),
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"HighBit": lambda x: str(int(x)) if (isinstance(x, float) and x*1==x) else str(x),
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"WindowCenter": lambda x: np.median(parse_float_tuples(x)),
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"FieldOfViewOrigin":parse_float_tuples,
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"EstimatedRadiographicMagnificationFactor": lambda x: x,
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"ContentTime": lambda x: x,
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"FieldOfViewRotation": lambda x: float(parse_float(x)),
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"KVP": lambda x: float(parse_float(x)),
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"ShutterLowerHorizontalEdge": lambda x: float(parse_float(x)),
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"ShutterRightVerticalEdge": lambda x: float(parse_float(x)),
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"XRayTubeCurrentInuA": lambda x: float(parse_float(x)),
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"RelativeXRayExposure": lambda x: float(parse_float(x)),
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"ManufacturerModelName": lambda x: str(x).lower().replace('"',''),
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"Manufacturer": lambda x: str(x).lower().replace('"','').replace(',', '').replace(" inc", "").rstrip('.'),
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"BodyPartThickness":lambda x: float(parse_float(x)),
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"CollimatorLeftVerticalEdge": lambda x: float(parse_float(x)),
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"CollimatorLowerHorizontalEdge": lambda x: float(parse_float(x)),
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"DetectorActiveDimensions" : lambda x: parse_float_tuples(x.replace("\\", ", ") if isinstance(x, str) else x),
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"ExposureTime": lambda x: x,
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"ExposuresOnDetectorSinceLastCalibration": lambda x: x,
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"ExposuresOnDetectorSinceManufactured": lambda x: x,
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"DistanceSourceToEntrance": lambda x: x,
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"DetectorTemperature":lambda x: float(parse_float(x)),
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"DistanceSourceToDetector": lambda x: x,
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}
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dtypes = {"0_ViewCodeSequence__0_ViewModifierCodeSequence_CodeMeaning": str,
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"0_ViewCodeSequence_CodeValue": str,
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"Grid": str,
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"HighBit": str, # int
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"WindowCenter": int,
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"FieldOfViewOrigin": 'O',
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"EstimatedRadiographicMagnificationFactor": float,
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"ContentTime": float, #NaN
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"FieldOfViewRotation": float,
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"KVP": float,
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"ShutterLowerHorizontalEdge": float,
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"ShutterRightVerticalEdge": float,
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"XRayTubeCurrentInuA": float,
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"RelativeXRayExposure": float,
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"ManufacturerModelName": str,
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"Manufacturer": str,
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"BodyPartThickness": float,
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"CollimatorLeftVerticalEdge": float,
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"CollimatorLowerHorizontalEdge": float,
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"DetectorActiveDimensions" : 'O',
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"ExposureTime": float,
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"ExposuresOnDetectorSinceLastCalibration": float, # NaNs
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"ExposuresOnDetectorSinceManufactured": float, # NaNs
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"DistanceSourceToEntrance": float,
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"DetectorTemperature": float,
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"DistanceSourceToDetector": float,
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}
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#cell#
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set(dffeatures.columns) - set(normalize_fun.keys())
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#cell#
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for kk, vv in dffeatures.items():
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print(kk)
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dffeatures.loc[:,kk] = vv.map(normalize_fun[kk]).astype(dtypes[kk])
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dffeatures.to_csv(outfn, sep='\t', compression='gzip')
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