Converting RGB dicom images to grayscale

Thiago Franco de Moraes
1 parent 298c9f95
Showing 3 changed files with 15 additions and 3 deletions Show diff stats
invesalius/control.py
invesalius/data/imagedata_utils.py
invesalius/reader/dicom.py
@@ -508,6 +508,7 @@ class Controller():
         self.ImportGroup(group, use_gui)
     def ImportGroup(self, group, gui=True):
+
         matrix, matrix_filename, dicom = self.OpenDicomGroup(group, 0, [0, 0], gui=gui)
         self.CreateDicomProject(dicom, matrix, matrix_filename)
@@ -878,6 +879,13 @@ class Controller():
     def OnOpenDicomGroup(self, group, interval, file_range):
+        dicom = group.GetDicomSample()
+        samples_per_pixel = dicom.image.samples_per_pixel
+        print(f"\n\n\n\n{samples_per_pixel =}\n\n\n")
+        if samples_per_pixel == 3:
+            dlg = wx.MessageDialog(wx.GetApp().GetTopWindow(), _("this is a rgb image, it's necessary to convert to grayscale to open on invesalius.\ndo you want to convert it to grayscale?"), _("Confirm"), wx.YES_NO | wx.YES_DEFAULT | wx.ICON_QUESTION)
+            if dlg.ShowModal() != wx.ID_YES:
+                return
         matrix, matrix_filename, dicom = self.OpenDicomGroup(group, interval, file_range, gui=True)
         self.CreateDicomProject(dicom, matrix, matrix_filename)
         self.LoadProject()
@@ -918,9 +926,9 @@ class Controller():
         xyspacing = dicom.image.spacing
         orientation = dicom.image.orientation_label
         samples_per_pixel = dicom.image.samples_per_pixel
-
         print(f"\n\n\n\n{samples_per_pixel =}\n\n\n")
+
         wl = float(dicom.image.level)
         ww = float(dicom.image.window)
@@ -39,6 +39,7 @@ import invesalius.reader.bitmap_reader as bitmap_reader
 import invesalius.utils as utils
 from invesalius import inv_paths
 from invesalius.data import vtk_utils as vtk_utils
+from skimage.color import rgb2gray
 if sys.platform == "win32":
     try:
@@ -483,10 +484,13 @@ def dcmmf2memmap(dcm_file, orientation):
     image = reader.GetImage()
     xs, ys, zs = image.GetSpacing()
     pf = image.GetPixelFormat()
+    samples_per_pixel = pf.GetSamplesPerPixel()
     np_image = converters.gdcm_to_numpy(image, pf.GetSamplesPerPixel() == 1)
+    if samples_per_pixel == 3:
+        np_image = image_normalize(rgb2gray(np_image), 0, 255)
+        print(f"\n\n\n{np_image.min() =} - {np_image.max() =}\n\n\n")
     temp_file = tempfile.mktemp()
     matrix = numpy.memmap(temp_file, mode="w+", dtype="int16", shape=np_image.shape)
-    print("Number of dimensions", np_image.shape)
     z, y, x = np_image.shape
     if orientation == "CORONAL":
         spacing = xs, zs, ys
@@ -962,7 +962,7 @@ class Parser():
         if not data:
             return 1
-        return data
+        return int(data)
     def GetPhotometricInterpretation(self):
         """
	@@ -962,7 +962,7 @@ class Parser():		@@ -962,7 +962,7 @@ class Parser():
962		962
963	if not data:	963	if not data:
964	return 1	964	return 1
965	- return data	965	+ return int(data)
966		966
967	def GetPhotometricInterpretation(self):	967	def GetPhotometricInterpretation(self):
968	"""	968	"""