https://github.com/Radiomics/pyradiomics
Revision 218954ddee91cc2279fb3b7ee7f7593052ed24c7 authored by Joost van Griethuysen on 20 March 2017, 16:40:48 UTC, committed by Joost van Griethuysen on 20 March 2017, 17:21:48 UTC
When building the wheel, parameter schema file was not included in the install. Move these files to a new subdirectory of pyradiomics and include them as "package_data".
1 parent d9dd283
Tip revision: 218954ddee91cc2279fb3b7ee7f7593052ed24c7 authored by Joost van Griethuysen on 20 March 2017, 16:40:48 UTC
BUG: Data_files not included in wheel distribution
BUG: Data_files not included in wheel distribution
Tip revision: 218954d
GenerateInputCSV_Datasethierarchy.py
from __future__ import print_function
import csv
import os
from DatasetHierarchyReader import DatasetHierarchyReader
def main():
DATA_ROOT_PATH = r''
inputDirectory = DATA_ROOT_PATH + r''
outputFile = DATA_ROOT_PATH + r'/FileList.csv'
filetype = '.nrrd'
keywordSettings = {}
keywordSettings['image'] = ''
keywordSettings['imageExclusion'] = 'label'
keywordSettings['mask'] = 'label'
keywordSettings['maskExclusion'] = ''
print("Scanning files...")
datasetReader = DatasetHierarchyReader(inputDirectory, filetype=filetype)
datasetHierarchyDict = datasetReader.ReadDatasetHierarchy()
print("Found %s patients, writing csv" % (str(len(datasetHierarchyDict.keys()))))
try:
with open(outputFile, 'wb') as outFile:
cw = csv.writer(outFile, lineterminator='\n')
for patientIndex, patientDirectory in enumerate(datasetHierarchyDict):
patientID = os.path.basename(patientDirectory)
for studyDirectory in datasetHierarchyDict[patientDirectory]:
studyDate = os.path.basename(studyDirectory)
imageFilepaths = datasetHierarchyDict[patientDirectory][studyDirectory]["reconstructions"]
maskFilepaths = datasetHierarchyDict[patientDirectory][studyDirectory]["segmentations"]
imageFilepath, maskFilepath = datasetReader.findImageAndLabelPair(imageFilepaths, maskFilepaths,
keywordSettings)
if (imageFilepath is not None) and (maskFilepath is not None):
# ReaderName is not extracted using DatasetHierarchyReader, set it to 'N/A'
cw.writerow([patientID, studyDate, 'N/A', imageFilepath, maskFilepath])
except Exception as exc:
print(exc)
if __name__ == '__main__':
main()
![swh spinner](/static/img/swh-spinner.gif)
Computing file changes ...