Dicom convert

bin/gt_image_convert

@@ -56,6 +56,7 @@ def gt_image_convert(input, output, pixeltype, flip, accessionnumber, **kwargs):
         inputImages.append(itk.imread(input[0]))
     else:
         series = gt.separate_series(input)
+        series = gt.separate_sequenceName_series(series)
         if accessionnumber:
             series = gt.separate_accessionNumber_series(series)
         for serie in series.keys():

gatetools/image_convert.py

@@ -82,6 +82,8 @@ def read_dicom_properties(self, slice, nextSlice=None):
             ip = slice[0x20, 0x32].value #Image Position
         elif Tag(0x54, 0x22) in slice and len(slice[0x54, 0x22].value) >0 and Tag(0x20, 0x32) in slice[0x54, 0x22][0]:
             ip = slice[0x54, 0x22][0][0x20, 0x32].value #Image Position
+        if ip == None:
+            ip = [0.0, 0.0, 0.0]
         self.origin = [ip[0], ip[1], ip[2]]
         if Tag(0x20, 0x37) in slice:
             self.io = slice[0x20, 0x37].value #Image Orientation
@@ -134,6 +136,26 @@ def separate_accessionNumber_series(series):
             files[new_key].append(file)
     return files
 
+def separate_sequenceName_series(series):
+    """
+    Read dicom and return a dictionary with the different series separated
+    """
+    files = {}
+    #Load dicom files
+    for serie in series.keys():
+        for file in series[serie]:
+            try:
+                sequenceName = pydicom.read_file(file)[0x0018, 0x0024].value
+            except pydicom.errors.InvalidDicomError:
+                ds = pydicom.read_file(file, force=True)
+                ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
+                sequenceName = ds[0x0018, 0x0024].value
+            new_key = str(serie) + "_" + str(sequenceName)
+            if new_key  not in files:
+                files[new_key] = []
+            files[new_key].append(file)
+    return files
+
 def read_dicom(dicomFiles):
     """
 
@@ -187,8 +209,7 @@ def read_dicom(dicomFiles):
         dicomProperties.read_dicom_properties(slices[0])
 
     # create 3D array
-    dicomProperties.img_shape[0] = len(slices)
-    dicomProperties.img_shape.append(slices[0].pixel_array.shape[0])
+    dicomProperties.img_shape = [len(slices)] + dicomProperties.img_shape
     img3d = np.float32(np.zeros(dicomProperties.img_shape))
 
     # fill 3D array with the images from the files

gatetools/roi_utils.py

@@ -363,20 +363,21 @@ def __init__(self,ds=None,roi_id=None,verbose=False, contours_list = None):
         for contour in roi.ContourSequence:
             ref = contour.ContourImageSequence[0].ReferencedSOPInstanceUID
             npoints = int(contour.NumberOfContourPoints)
-            # check assumption on number of contour coordinates
-            assert(len(contour.ContourData)==3*npoints)
-            points = np.array([float(coord) for coord in contour.ContourData]).reshape(npoints,3)
-            zvalues = set(points[:,2])
-            # check assumption that all points are in the same xy plane (constant z)
-            assert(len(zvalues)==1)
-            zvalue = zvalues.pop()
-            if zvalue in self.zlist:
-                ic = self.zlist.index(zvalue)
-                self.contour_layers[ic].add_contour(points,ref)
-            else:
-                self.contour_layers.append(contour_layer(points,ref))
-                self.zlist.append(zvalue)
-            self.bb.should_contain_all(points)
+            if npoints > 2:
+                # check assumption on number of contour coordinates
+                assert(len(contour.ContourData)==3*npoints)
+                points = np.array([float(coord) for coord in contour.ContourData]).reshape(npoints,3)
+                zvalues = set(points[:,2])
+                # check assumption that all points are in the same xy plane (constant z)
+                assert(len(zvalues)==1)
+                zvalue = zvalues.pop()
+                if zvalue in self.zlist:
+                    ic = self.zlist.index(zvalue)
+                    self.contour_layers[ic].add_contour(points,ref)
+                else:
+                    self.contour_layers.append(contour_layer(points,ref))
+                    self.zlist.append(zvalue)
+                self.bb.should_contain_all(points)
         if verbose:
             logger.info("roi {}={} has {} points on {} contours with z range [{},{}]".format(
                     self.roinr,self.roiname,self.npoints_total,self.ncontours,self.bb.zmin,self.bb.zmax))