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@@ -8,15 +8,15 @@ import sys
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shome=os.path.expanduser('~nixUser')
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fhome=os.path.expanduser('~')
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-with open(os.path.join(fhome,".labkey","setup.json"),"w") as f:
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+with open(os.path.join(fhome,".labkey","setup.json")) as f:
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setup=json.load(f)
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-sys.path.insert(1,setup["paths"]["labkeyInterface"])
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+sys.path.insert(0,setup["paths"]["labkeyInterface"])
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import labkeyInterface
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import labkeyDatabaseBrowser
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import labkeyFileBrowser
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-sys.path.insert(1,setup["paths"]["orthancInterface"])
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+sys.path.insert(0,setup["paths"]["orthancInterface"])
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import orthancInterface
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import orthancFileBrowser
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@@ -47,13 +47,13 @@ ofb=orthancFileBrowser.orthancFileBrowser(onet)
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hi=0
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project='iPNUMMretro/Study'
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dataset='Imaging'
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-h
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tempBase=os.path.join(fhome,'temp')
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#all images from database
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ds=db.selectRows(project,'study',dataset,[])
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-imageSelector={"CT":"CT","PETWB":"PET"};
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-imageResampledField={"CT":"ctResampled","PETWB":"petResampled"}
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+#imageSelector={"CT":"CT","PET":"PETWB"};
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+imageSelector={"CT":"CT_orthancId","PET":"PETWB_orthancId"}
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+imageResampledField={"CT":"ctResampled","PET":"petResampled"}
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#projectNIfTIBase=os.path.join(labkeyBase,'files',project,'@files/nifti')
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#use webdav to transfer file (even though it is localhost)
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@@ -92,12 +92,12 @@ def getDicom(ofb,row,zipDir,rawDir,im,imageSelector):
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#Return True for valid outcome and False for troubles in row formating or unzip failures
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- seriesId=row[im];
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+ seriesId=row[imageSelector[im]];
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if seriesId=="0":
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return False
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print("{}: {}".format(im,seriesId))
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- fname=os.path.join(zipDir,getStudyLabel(row)+'_'+imageSelector[im]+".zip");
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+ fname=os.path.join(zipDir,getStudyLabel(row)+'_'+im+".zip");
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#copy data from orthanc
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if os.path.isfile(fname):
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@@ -108,7 +108,7 @@ def getDicom(ofb,row,zipDir,rawDir,im,imageSelector):
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#unzip the zipped dicom series
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- unzipDir=os.path.join(rawDir,imageSelector[im])
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+ unzipDir=os.path.join(rawDir,im)
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if os.path.isdir(unzipDir):
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print("Data already unzipped")
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@@ -142,7 +142,7 @@ for row in ds["rows"]:
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#interesting files are processedDir/studyName_CT_notCropped_2mmVoxel.nii
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#asn processedDir/studyName_PET_notCropped_2mmVoxel.nii
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volumeFileNames={im:\
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- getStudyLabel(row)+'_'+imageSelector[im]+
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+ getStudyLabel(row)+'_'+im+
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'_notCropped_2mmVoxel.nii'\
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for im in imageSelector}
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gzFileNames={im:f+".gz" \
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@@ -187,7 +187,7 @@ for row in ds["rows"]:
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#specify local file names with path
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volumeFiles={im:os.path.join(processedDir,f)\
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- for (im.f) in volumeFileNames.items()}
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+ for (im,f) in volumeFileNames.items()}
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gzFiles={im:f+".gz"\
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for (im,f) in volumeFiles.items()}
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Andrej Studen/Merlin