RadiomicsModellingSuite 0.0.0__tar.gz

radiomicsmodellingsuite-0.0.0/LICENSE

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+��

radiomicsmodellingsuite-0.0.0/MANIFEST.in

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+include RadiomicsModellingSuite/config.yml
+include README.md

radiomicsmodellingsuite-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: RadiomicsModellingSuite
+Version: 0.0.0
+Summary: Details about the package
+Author: AllisonNg067
+Author-email: allison.ng@uwa.edu.au
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: asttokens==3.0.0
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+Dynamic: author
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+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
+
+ÿþ

radiomicsmodellingsuite-0.0.0/README.md

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+��

radiomicsmodellingsuite-0.0.0/RadiomicsModellingSuite/__init__.py

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+# Define the __all__ variable
+__all__ = ["acquisition_parameters", "data_processing", "dataset_manipulation", "exploratory_analysis", 
+           "feature_extraction", "feature_harmonisation", "feature_selection", "image_processing", 
+           "latex_reporting", "model_calibration", "model_evaluation", "model_explainability", 
+           "model_training", "radiomics_modelling_suite", "string_formatting"]
+
+from . import acquisition_parameters
+from . import data_processing
+from . import dataset_manipulation
+from . import exploratory_analysis
+from . import feature_extraction
+from . import feature_harmonisation
+from . import feature_selection
+from . import image_processing
+from . import latex_reporting
+from . import model_calibration
+from . import model_evaluation
+from . import model_explainability
+from . import model_training
+from . import radiomics_modelling_suite
+from . import string_formatting

radiomicsmodellingsuite-0.0.0/RadiomicsModellingSuite/acquisition_parameters.py

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+import pydicom as dicom
+import numpy as np
+import os
+import pandas as pd
+import dicom2nifti
+from copy import deepcopy
+dicom2nifti.settings.disable_validate_slice_increment()
+from . import latex_reporting as lr
+from . import string_formatting as sf
+
+def obtain_acquisition_parameters(directory_list, scan_types, author, filename="acquisition_parameters.csv", max_string_length = 3, latex_sections=['Information', 'Paragraphs', 'all_tables', 'Tables']):
+  """
+    Function to obtain acquisition parameters from the dicom files in the directory_list
+
+    Parameters:
+        
+        * directory_list (list[str]) - list of directories containing the dicom slices
+        
+        * scan_types (list[str]) - list of scan types studied
+        
+        * author (str) - author name for latex report
+        
+        * filename (str) - filename to save acquisition parameters to
+        
+        * max_string_length (int) - maximum number of count values to write in a paragraph, if bigger than this maximum, 
+                                 the paragraph will be written as a table instead
+        
+        * latex_sections (list[str]) - list of sections to include in latex report
+    
+    Outputs:
+        
+        * csv file with acquisition parameters from each scan
+
+        * pdf and latex file with acquisition parameters
+    """
+  mri_acquisition_dict = {'Manufacturer': [], 'SeriesDescription': [], 'ManufacturerModelName': [], 'ContrastBolusAgent': [], 'ScanningSequence': [], 
+                      'SequenceVariant': [], 'ScanOptions': [], 'SliceThickness': [], 'ImagingFrequency': [], 'RepetitionTime': [], 'EchoTime': [], 'InversionTime': [], 
+                      'MagneticFieldStrength': [], 'NumberOfPhaseEncodingSteps': [], 'EchoTrainLength': [], 'ContrastBolusVolume': [], 'InPlanePhaseEncodingDirection': [], 
+                      'FlipAngle': [], 'PixelSpacing': [], 'SpacingBetweenSlices': [], 'dBdt': [], 'ImageDimensions': []} #dictionary to store acquisition parameters for MRI images
+  mri_numerical_keys = [key for key in mri_acquisition_dict.keys() if key not in ['Manufacturer', 'SeriesDescription', 'ManufacturerModelName', 'ContrastBolusAgent', 'ScanningSequence',
+                      'SequenceVariant', 'ScanOptions', 'InPlanePhaseEncodingDirection', 'PixelSpacing', 'ImageDimensions']] #list of keys which contain numerical values in MRI acquisition parameters
+  mri_paragraphs = [['Manufacturer', 'ManufacturerModelName', 'ContrastBolusAgent', 'ContrastBolusVolume'], ['ScanningSequence', 'ScanOptions', 'SequenceVariant'],
+                    ['ImagingFrequency', 'RepetitionTime', 'EchoTime', 'InversionTime', 
+                       'NumberOfPhaseEncodingSteps', 'EchoTrainLength', 'InPlanePhaseEncodingDirection', 
+                      'FlipAngle',], ['MagneticFieldStrength', 'dBdt'], 
+                       ['SliceThickness', 'SpacingBetweenSlices', 'PixelSpacing', 'ImageDimensions']]
+  pet_acquisition_dict = {'Manufacturer': [], 'SeriesDescription': [], 'ManufacturerModelName': [], 'SliceThickness': [], 
+                          'SoftwareVersions': [], 'TriggerTime': [], 'FrameTime': [], 'IntervalsAcquired': [], 'IntervalsRejected': [],
+                          'Reconstruction​Diameter': [], 'EnergyWindowLowerLimit': [], 'EnergyWindowUpperLimit': [], 'CorrectedImage': [],
+                          'RadiopharmaceuticalInformationSequence':[],'Radiopharmaceutical': [],'RadiopharmaceuticalVolume': [], 'RadionuclideTotalDose': [], 'RadionuclideHalfLife': [], 'RadionuclidePositronFraction': [],
+                          'SamplesPerPixel': [], 'RandomsCorrected': [], 'RandomsCorrectionMethod':[], 'AttenuationCorrectionMethod': [], 'DecayCorrection': [], 'ReconstructionMethod': [], 'SliceSensitivityFactor': [],
+                          'DecayFactor': [], 'DoseCalibrationFactor': [], 'ScatterFractionFactor': [], 'DeadTimeFactor': [],  'CoincidenceWindowWidth':[],
+                          'CollimatorType': [], 'GantryDetectorTilt': [],
+                       'PixelSpacing': [], 'SpacingBetweenSlices': [],  'ImageDimensions': []} #dictionary to store acquisition parameters for PET images
+  pet_paragraphs = [['Manufacturer', 'ManufacturerModelName', 'SoftwareVersions', 'ReconstructionMethod'], ['TriggerTime', 'FrameTime', 'IntervalsAcquired', 'IntervalsRejected',
+                          'Reconstruction​Diameter', 'EnergyWindowLowerLimit', 'EnergyWindowUpperLimit', 'CorrectedImage'],
+                          ['RadiopharmaceuticalInformationSequence', 'Radiopharmaceutical','RadiopharmaceuticalVolume', 'RadionuclideTotalDose', 'RadionuclideHalfLife', 'RadionuclidePositronFraction'],
+                          ['SamplesPerPixel','RandomsCorrected', 'RandomsCorrectionMethod', 'AttenuationCorrectionMethod', 'DecayCorrection', 'SliceSensitivityFactor',
+                          'DecayFactor', 'DoseCalibrationFactor', 'ScatterFractionFactor', 'DeadTimeFactor', 'CoincidenceWindowWidth'],
+                          ['CollimatorType', 'GantryDetectorTilt'],
+                          ['SliceThickness', 'SpacingBetweenSlices', 'PixelSpacing', 'ImageDimensions']]
+  pet_numerical_keys = [key for key in pet_acquisition_dict.keys() if key not in ['Manufacturer', 'SeriesDescription', 'ManufacturerModelName', 'SoftwareVersions', 
+                                                                                  'PixelSpacing', 'ImageDimensions', 'CorrectedImage', 'RadiopharmaceuticalInformationSequence', 'Radiopharmaceutical', 'ReconstructionMethod', 
+                                                                                  'AttenuationCorrectionMethod', 'RandomsCorrectionMethod', 'DecayCorrection',
+                                                                                  'CollimatorType']] #list of keys which contain numerical values in PET acquisition parameters
+  ct_acquisition_dict = {'Manufacturer': [], 'SeriesDescription': [], 'ManufacturerModelName': [], 'SliceThickness': [], 'ScanOptions': [],
+                          'KVP': [], 'SoftwareVersions': [], 'DataCollectionDiameter': [], 'Reconstruction​Diameter': [], 'ReconstructionMethod': [], 'DistanceSourceToDetector': [],
+                          'DistanceSourceToPatient': [], 'RotationDirection': [], 'ExposureTime': [], 'XRayTubeCurrent': [], 'Exposure': [], 'FilterType': [],
+                          'GeneratorPower': [], 'FocalSpots': [], 'ConvolutionKernel': [], 'RevolutionTime': [],
+                          'SingleCollimationWidth': [], 'TotalCollimationWidth': [], 'TableSpeed': [], 'TableFeedPerRotation': [], 'SpiralPitchFactor': [],
+                       'PixelSpacing': [], 'SpacingBetweenSlices': [],  'ImageDimensions': []} #dictionary to store acquisition parameters for CT images
+  ct_paragraphs = [['Manufacturer', 'ManufacturerModelName', 'SoftwareVersions', 'ReconstructionMethod', 'ScanOptions'], 
+                          ['DataCollectionDiameter', 'Reconstruction​Diameter', 'DistanceSourceToDetector',
+                          'DistanceSourceToPatient', 'ConvolutionKernel'], ['RevolutionTime', 'RotationDirection',
+                          'SingleCollimationWidth', 'TotalCollimationWidth', 'TableSpeed', 'TableFeedPerRotation', 'SpiralPitchFactor'],
+                          ['KVP','ExposureTime', 'XRayTubeCurrent', 'Exposure', 'FilterType', 'GeneratorPower', 'FocalSpots'],
+                          ['SliceThickness', 'SpacingBetweenSlices', 'PixelSpacing', 'ImageDimensions']]
+  ct_numerical_keys = [key for key in ct_acquisition_dict.keys() if key not in ['Manufacturer', 'SeriesDescription', 'ManufacturerModelName', 'ScanOptions', 
+                                                                                'ReconstructionMethod', 'SoftwareVersions', 'RotationDirection', 'FilterType', 'ConvolutionKernel', 'PixelSpacing', 'ImageDimensions', 'CorrectedImage']] #list of keys which contain numerical values in CT acquisition parameters
+  directories_list = list(np.transpose(np.array(directory_list))) 
+  directories_list = [list(item) for item in directories_list]
+  for i, directories in enumerate(directories_list):
+      scan_type = scan_types[i]
+      
+# Initialize a fresh acquisition_dict for each scan_type
+      acquisition_dict = {}
+      numerical_keys = []
+
+      for j, directory in enumerate(directories):
+        dicom_path = os.path.join(directory, os.listdir(directory)[0]) #get the first dicom file in the folder path
+        ds = dicom.dcmread(dicom_path) #extract the dicom dataset from the dicom file
+        if ds['Modality'].value == 'MR' and j == 0: #check modality of dicom images and define acquisition dictionary and numerical keys appropriately
+          acquisition_dict = deepcopy(mri_acquisition_dict)
+          numerical_keys = mri_numerical_keys
+          paragraphs = mri_paragraphs
+        elif ds['Modality'].value == 'PT' and j == 0:
+          acquisition_dict = deepcopy(pet_acquisition_dict)
+          numerical_keys = pet_numerical_keys
+          paragraphs = pet_paragraphs
+        elif ds['Modality'].value == 'CT' and j == 0:
+          acquisition_dict = deepcopy(ct_acquisition_dict)
+          numerical_keys = ct_numerical_keys
+          paragraphs = ct_paragraphs       
+        keys_list = [elem.keyword for elem in ds] #get the list of keys which are present in the dicom dataset
+        missing_keys = [key for key in acquisition_dict.keys() if key not in keys_list + ['ImageDimensions']] #check which keys are missing from the dicom dataset
+        for elem in ds:
+          if elem.keyword in acquisition_dict.keys():
+            acquisition_dict[elem.keyword].append(elem.value)
+        if missing_keys != []:
+          #if there are missing keys, append None to the dictionary
+          for key in missing_keys:
+            if key in numerical_keys:
+              acquisition_dict[key].append(np.nan)
+            else:
+              acquisition_dict[key].append(None) #append empty string for missing keys
+        shape = list(ds.pixel_array.shape) #get the shape of the pixel array for each slice
+        shape = [len(os.listdir(directory))] + shape #append the number of slices to the shape
+        acquisition_dict['ImageDimensions'].append(tuple(shape)) #append the shape to the dictionary
+      df = pd.DataFrame.from_dict(acquisition_dict) #convert the dictionary to a dataframe
+      for label, content in df.items():
+        if content.value_counts().to_string(name=False) != "Series([], )" and label not in numerical_keys:
+          df.loc[:, label] = content.replace(r'^\s*$', pd.NA, regex=True).fillna("Unspecified") #fill in missing categorical values
+      df.to_csv(scan_type + "_" + filename, index=False) #save the dataframe to a csv file
+      df = sf.clean_string_columns(df, numerical_keys)     
+# Apply to the entire column
+      if 'ContrastBolusAgent' in df.columns:
+        df['ContrastBolusAgent'] = df['ContrastBolusAgent'].apply(sf.format_contrast_label)
+      get_acquisition_text(df, scan_type, numerical_keys) #get the unique acquisition parameters and save it as a text file
+      lr.acquisition_latex(author, df, paragraphs, numerical_keys, sections=latex_sections, max_string_length=max_string_length, filename=scan_type+'_acquisition')
+      
+def write_acquisition_text(acquisition_df, numerical_keys, series_description = True, verbose = True):
+   """
+    Extracts text of acquisition parameters from the dataframe
+
+    Parameters:
+        
+        * acquisition_df (pandas.DataFrame): dataframe with acquisition parameters
+        
+        * numerical_keys (list): list of keys containing numerical values
+        
+        * series_description (boolean): if True, write SeriesDescription to file
+        
+        * verbose (boolean): if True, write text with unique acquisition parameters and counts, otherwise summary statistics only are provided for numerical parameters
+
+    Returns:
+        
+        * acquisition_text (str): text with unique acquisition parameters and counts
+    """ 
+   acquisition_text = "" #initialise text string
+   for label, content in acquisition_df.items(): #loop through each scan in dataframe
+      if label == 'SeriesDescription' and not series_description: #skip SeriesDescription if series_description is False
+         continue
+      if content.value_counts().to_string(name=False) != "Series([], )":
+         acquisition_text += (str(label) + ':\n')  # Write the label of the acquisition parameter
+         if str(label) in numerical_keys and not verbose: #check if current label is numerical and verbose is False
+            content = content.apply(lambda x: str(x) if isinstance(x, dicom.sequence.Sequence) else x)
+            unique_values = content.dropna().unique()
+            if len(unique_values) == 1:
+              acquisition_text += (str(unique_values[0]) + '\n')  # If there is only one unique value, write it 
+            else:
+              #calculate mean, std, min and max for numerical values
+              mean = np.nanmean(content)
+              median = np.nanmedian(content)
+              std = np.nanstd(content)
+              min = np.nanmin(content)
+              max = np.nanmax(content)
+              #write mean, std, and range to the text
+              acquisition_text += ('Mean: ' + str(mean) + '\n')
+              acquisition_text += ('Median: ' + str(median) + '\n')
+              acquisition_text += ('Standard Deviation: ' + str(std) + '\n')
+              acquisition_text += ('Range: [' + str(min) + ' - ' + str(max) + ']\n')
+         else:
+            acquisition_text += (content.value_counts().to_string(name=False) + '\n')  # Write the unique values and their counts
+         acquisition_text += '\n' # Add a newline for better readability
+   return acquisition_text     
+
+def get_acquisition_text(acquisition_df, scan_type, numerical_keys):
+  """
+    Saves acquisition parameters from the dataframe to text files - both as a whole dataset and divided into scan types
+
+    Parameters:
+        
+        * acquisition_df (pandas.DataFrame): dataframe with acquisition parameters
+        
+        * scan_type (str): scan type to extract acquisition parameters for
+        
+        * numerical_keys (list): list of keys containing numerical values
+
+    Output:
+        
+        * text file detailing acquisition parameters from entire dataset, as well as a text file for each series description present
+    """  
+  descriptors = acquisition_df["SeriesDescription"].unique() #obtain list of unique series descriptions
+  for descriptor in descriptors: #loop through each descriptor
+    filtered_descriptor = descriptor.replace(":", "")
+    verbose_filename = sf.clean_filename(filtered_descriptor.replace(" ", "_") + "_verbose_acquisition_parameters.txt")
+    acquisition_filename = sf.clean_filename(filtered_descriptor.replace(" ", "_") + "_acquisition_parameters.txt")
+    df = acquisition_df[acquisition_df['SeriesDescription'] == descriptor] #filter dataframe to just have elements with that description
+    verbose_acquisition_text = ("Scan Type: " + str(descriptor) + ':\n')  # Write the scan type
+    acquisition_text = ("Scan Type: " + str(descriptor) + ':\n')  # Write the scan type
+    verbose_acquisition_text += write_acquisition_text(df, numerical_keys, series_description = False)
+    acquisition_text += write_acquisition_text(df, numerical_keys, series_description = False, verbose=False)
+    with open(verbose_filename, 'w') as f:  # Save the verbose acquisition text to a file
+      f.write(verbose_acquisition_text)  # Write the verbose acquisition text to the file
+    with open(acquisition_filename, 'w') as f:  # Save the acquisition text to a file
+      f.write(acquisition_text)  # Write the acquisition text to the file
+  #get text for entire dataset and save it
+  full_verbose_acquisition = write_acquisition_text(acquisition_df, numerical_keys)
+  full_acquisition = write_acquisition_text(acquisition_df, numerical_keys, verbose=False)
+  with open(scan_type + "_verbose_acquisition_parameters.txt", "w") as f:
+     f.write(full_verbose_acquisition)
+  with open(scan_type + "_acquisition_parameters.txt", "w") as f:
+     f.write(full_acquisition)