Merge pull request #89 from OpenGATE/pydicom

Pydicom change dcm_read to dcmread
OpenGATE · Oct 31, 2024 · 2e2141c · 2e2141c
2 parents 9381cea + ed6adb2
commit 2e2141c
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Showing 6 changed files with 24 additions and 28 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -17,7 +17,6 @@ jobs:
       fail-fast: false
       matrix:
         python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
-        ITK_VERSION: [5.3.0, pre]
 
     steps:
     - name: Checkout github repo
@@ -33,10 +32,7 @@ jobs:
     - name: Install dependencies
       run: |
           python -m pip install --upgrade pip
-          if [ ${{ matrix.ITK_VERSION }} == 'pre' ];
-              then pip install itk --pre;
-              else pip install itk==${{ matrix.ITK_VERSION }};
-          fi
+          pip install itk
           pip install -e .
           pip install uproot3
           pip freeze

diff --git a/bin/gt_dicom_rt_struct_to_image b/bin/gt_dicom_rt_struct_to_image
@@ -40,7 +40,7 @@ def gt_dicom_rt_struct_to_image(list_roi, filename_struct, filename_img, roi, cr
     gt.logging_conf(verbose=(verbose or list_roi),logfile=logfile)
 
     # read dicom struct
-    structset = pydicom.read_file(filename_struct, force=True)
+    structset = pydicom.dcmread(filename_struct, force=True)
 
     # print roi names
     roi_names = gt.list_roinames(structset)

diff --git a/gatetools/dvh.py b/gatetools/dvh.py
@@ -104,7 +104,7 @@ def test_dvh(self):
         logger.info('Test_DVH test_dvh')
         tmpdirpath = tempfile.mkdtemp()
         filenameStruct = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtstruct.dcm?inline=false", out=tmpdirpath, bar=None)
-        structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
+        structset = pydicom.dcmread(os.path.join(tmpdirpath, filenameStruct))
         filenameDose = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtdose.dcm?inline=false", out=tmpdirpath, bar=None)
         doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
         transformImage = gt.applyTransformation(input=doseImage, neworigin=[-176, -320, -235])
@@ -123,7 +123,7 @@ def test_dvh_volume(self):
         logger.info('Test_DVH test_dvh_volume')
         tmpdirpath = tempfile.mkdtemp()
         filenameStruct = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtstruct.dcm?inline=false", out=tmpdirpath, bar=None)
-        structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
+        structset = pydicom.dcmread(os.path.join(tmpdirpath, filenameStruct))
         filenameDose = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtdose.dcm?inline=false", out=tmpdirpath, bar=None)
         doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
         transformImage = gt.applyTransformation(input=doseImage, neworigin=[-176, -320, -235])
@@ -141,7 +141,7 @@ def test_dvh_compute_v(self):
         logger.info('Test_DVH test_dvh_compute_v')
         tmpdirpath = tempfile.mkdtemp()
         filenameStruct = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtstruct.dcm?inline=false", out=tmpdirpath, bar=None)
-        structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
+        structset = pydicom.dcmread(os.path.join(tmpdirpath, filenameStruct))
         filenameDose = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtdose.dcm?inline=false", out=tmpdirpath, bar=None)
         doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
         transformImage = gt.applyTransformation(input=doseImage, neworigin=[-176, -320, -235])
@@ -156,7 +156,7 @@ def test_dvh_compute_d(self):
         logger.info('Test_DVH test_dvh_compute_d')
         tmpdirpath = tempfile.mkdtemp()
         filenameStruct = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtstruct.dcm?inline=false", out=tmpdirpath, bar=None)
-        structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
+        structset = pydicom.dcmread(os.path.join(tmpdirpath, filenameStruct))
         filenameDose = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtdose.dcm?inline=false", out=tmpdirpath, bar=None)
         doseImage = gt.read_3d_dicom([os.path.join(tmpdirpath, filenameDose)])
         transformImage = gt.applyTransformation(input=doseImage, neworigin=[-176, -320, -235])

diff --git a/gatetools/image_convert.py b/gatetools/image_convert.py
@@ -105,9 +105,9 @@ def separate_series(dicomFiles):
     #Load dicom files
     for file in dicomFiles:
         try:
-            seriesInstanceUID = pydicom.read_file(file)[0x0020, 0x000e].value
+            seriesInstanceUID = pydicom.dcmread(file)[0x0020, 0x000e].value
         except pydicom.errors.InvalidDicomError:
-            ds = pydicom.read_file(file, force=True)
+            ds = pydicom.dcmread(file, force=True)
             ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
             seriesInstanceUID = ds[0x0020, 0x000e].value
             print(seriesInstanceUID)
@@ -125,9 +125,9 @@ def separate_accessionNumber_series(series):
     for serie in series.keys():
         for file in series[serie]:
             try:
-                accessionNumber = pydicom.read_file(file)[0x0020, 0x0012].value
+                accessionNumber = pydicom.dcmread(file)[0x0020, 0x0012].value
             except pydicom.errors.InvalidDicomError:
-                ds = pydicom.read_file(file, force=True)
+                ds = pydicom.dcmread(file, force=True)
                 ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
                 accessionNumber = ds[0x0020, 0x0012].value
             new_key = str(serie) + "_" + str(accessionNumber)
@@ -145,9 +145,9 @@ def separate_sequenceName_series(series):
     for serie in series.keys():
         for file in series[serie]:
             try:
-                sequenceName = pydicom.read_file(file)[0x0018, 0x0024].value
+                sequenceName = pydicom.dcmread(file)[0x0018, 0x0024].value
             except pydicom.errors.InvalidDicomError:
-                ds = pydicom.read_file(file, force=True)
+                ds = pydicom.dcmread(file, force=True)
                 ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
                 sequenceName = ds[0x0018, 0x0024].value
             new_key = str(serie) + "_" + str(sequenceName)
@@ -165,9 +165,9 @@ def read_dicom(dicomFiles):
     #Load dicom files
     for file in dicomFiles:
         try:
-            files.append(pydicom.read_file(file))
+            files.append(pydicom.dcmread(file))
         except pydicom.errors.InvalidDicomError:
-            ds = pydicom.read_file(file, force=True)
+            ds = pydicom.dcmread(file, force=True)
             ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
             files.append(ds)
 
@@ -242,9 +242,9 @@ def read_3d_dicom(dicomFile, flip=False):
     """
     files = []
     try:
-        files.append(pydicom.read_file(dicomFile[0]))
+        files.append(pydicom.dcmread(dicomFile[0]))
     except pydicom.errors.InvalidDicomError:
-        ds = pydicom.read_file(dicomFile[0], force=True)
+        ds = pydicom.dcmread(dicomFile[0], force=True)
         ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
         files.append(ds)
 

diff --git a/gatetools/image_uncertainty.py b/gatetools/image_uncertainty.py
@@ -202,28 +202,28 @@ def test_image_uncertainty(self):
         xx, yy, zz = np.meshgrid(x, y, z)
         npImage = 10*xx+4.5
         npsImage = 10*xx**2+9*xx+2.85
-        image = itk.image_from_array(np.float32(npImage))
+        image = itk.image_from_array(np.float64(npImage))
         images = [image]
-        simage = itk.image_from_array(np.float32(npsImage))
+        simage = itk.image_from_array(np.float64(npsImage))
         simages = [simage]
         uncertainty = image_uncertainty(images, simages, N=1000000000000)
         tmpdirpath = tempfile.mkdtemp()
         itk.imwrite(uncertainty, os.path.join(tmpdirpath, "uncertainty.mha"))
         with open(os.path.join(tmpdirpath, "uncertainty.mha"),"rb") as fnew:
             bytesNew = fnew.read()
             new_hash = hashlib.sha256(bytesNew).hexdigest()
-            self.assertTrue("0a2dc7a0e28509c569cecde6b6252507936b29365cb4db0c75ab3c0fab3b2bc4" == new_hash)
-        shutil.rmtree(tmpdirpath)
+            self.assertTrue("0e1f8e0f0d7d7d3921c726dc33409345e6d9b8bfcc53b797d67f8b48997fa1a5" == new_hash)
+        print(tmpdirpath)
     def test_image_uncertainty_by_slice(self):
         x = np.arange(0, 1, 0.01)
         y = np.arange(0, 1, 0.01)
         z = np.arange(0, 1, 0.01)
         xx, yy, zz = np.meshgrid(x, y, z)
         npImage = 10*xx+4.5
         npsImage = 10*xx**2+9*xx+2.85
-        image = itk.image_from_array(np.float32(npImage))
+        image = itk.image_from_array(np.float64(npImage))
         images = [image]
-        simage = itk.image_from_array(np.float32(npsImage))
+        simage = itk.image_from_array(np.float64(npsImage))
         simages = [simage]
         uncertainty, mean, nb = image_uncertainty_by_slice(images, simages, N=1000000000000)
         tmpdirpath = tempfile.mkdtemp()
@@ -234,7 +234,7 @@ def test_image_uncertainty_by_slice(self):
         with open(os.path.join(tmpdirpath, "uncertainty.mha"),"rb") as fnew:
             bytesNew = fnew.read()
             new_hash = hashlib.sha256(bytesNew).hexdigest()
-            self.assertTrue("0a2dc7a0e28509c569cecde6b6252507936b29365cb4db0c75ab3c0fab3b2bc4" == new_hash)
+            self.assertTrue("0e1f8e0f0d7d7d3921c726dc33409345e6d9b8bfcc53b797d67f8b48997fa1a5" == new_hash)
         shutil.rmtree(tmpdirpath)
     def test_image_uncertainty_Poisson(self):
         x = np.arange(0, 1, 0.01)

diff --git a/gatetools/roi_utils.py b/gatetools/roi_utils.py
@@ -783,7 +783,7 @@ class Test_ROI(LoggedTestCase):
     def test_roi(self):
         tmpdirpath = tempfile.mkdtemp()
         filenameStruct = wget.download("https://gitlab.in2p3.fr/opengate/gatetools_data/-/raw/master/rtstruct.dcm?inline=false", out=tmpdirpath, bar=None)
-        structset = pydicom.read_file(os.path.join(tmpdirpath, filenameStruct))
+        structset = pydicom.dcmread(os.path.join(tmpdirpath, filenameStruct))
 
         # roi names
         roi_names = list_roinames(structset)