Single slice import (#207)

* Importing just one bitmap slice * Importing just one dicom slice

Single slice import (#207)
* Importing just one bitmap slice * Importing just one dicom slice
Thiago Franco de Moraes · GitHub
1 parent 4ed4823b
Showing 4 changed files with 34 additions and 25 deletions Show diff stats
invesalius/data/imagedata_utils.py
invesalius/data/slice_.py
invesalius/gui/import_panel.py
invesalius/reader/bitmap_reader.py
@@ -284,7 +284,8 @@ def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage
     returns it and its related filename.
     """
     message = _("Generating multiplanar visualization...")
-    update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
+    if len(files) > 1:
+        update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
     temp_file = tempfile.mktemp()
@@ -368,12 +369,14 @@ def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage
             array.shape = matrix.shape[1], matrix.shape[2]
             matrix[n] = array
-        update_progress(cont,message)
+        if len(files) > 1:
+            update_progress(cont,message)
         cont += 1
     matrix.flush()
     scalar_range = min_scalar, max_scalar
+    print("MATRIX", matrix.shape)
     return matrix, scalar_range, temp_file
@@ -382,8 +385,9 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
     From a list of dicom files it creates memmap file in the temp folder and
     returns it and its related filename.
     """
-    message = _("Generating multiplanar visualization...")
-    update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
+    if len(files) > 1:
+        message = _("Generating multiplanar visualization...")
+        update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type = "ProgressDialog")
     first_slice = read_dcm_slice_as_np2(files[0], resolution_percentage)
     slice_size = first_slice.shape[::-1]
@@ -410,7 +414,8 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
             matrix[:, :, n] = im_array
         else:
             matrix[n] = im_array
-        update_progress(n, message)
+        if len(files) > 1:
+            update_progress(n, message)
     matrix.flush()
     scalar_range = matrix.min(), matrix.max()
@@ -614,12 +614,20 @@ class Slice(with_metaclass(utils.Singleton, object)):
             final_image = self.do_blend(final_image, aux_image)
         return final_image
-    def get_image_slice(self, orientation, slice_number, number_slices=1,
-                        inverted=False, border_size=1.0):
-        if self.buffer_slices[orientation].index == slice_number \
-           and self.buffer_slices[orientation].image is not None:
+    def get_image_slice(
+        self,
+        orientation,
+        slice_number,
+        number_slices=1,
+        inverted=False,
+        border_size=1.0,
+    ):
+        dz, dy, dx = self.matrix.shape
+        if (
+            self.buffer_slices[orientation].index == slice_number
+            and self.buffer_slices[orientation].image is not None
+        ):
             n_image = self.buffer_slices[orientation].image
-            #  print "BUFFER IMAGE"
         else:
             if self._type_projection == const.PROJECTION_NORMAL:
                 number_slices = 1
@@ -642,7 +650,7 @@ class Slice(with_metaclass(utils.Singleton, object)):
                 if np.any(self.q_orientation[1::]):
                     transforms.apply_view_matrix_transform(self.matrix, self.spacing, M, slice_number, orientation, self.interp_method, self.matrix.min(), tmp_array)
                 if self._type_projection == const.PROJECTION_NORMAL:
-                    n_image = tmp_array.squeeze()
+                    n_image = tmp_array.reshape(dy, dx)
                 else:
                     if inverted:
                         tmp_array = tmp_array[::-1]
@@ -690,7 +698,7 @@ class Slice(with_metaclass(utils.Singleton, object)):
                     transforms.apply_view_matrix_transform(self.matrix, self.spacing, M, slice_number, orientation, self.interp_method, self.matrix.min(), tmp_array)
                 if self._type_projection == const.PROJECTION_NORMAL:
-                    n_image = tmp_array.squeeze()
+                    n_image = tmp_array.reshape(dz, dx)
                 else:
                     #if slice_number == 0:
                         #slice_number = 1
@@ -740,7 +748,7 @@ class Slice(with_metaclass(utils.Singleton, object)):
                     transforms.apply_view_matrix_transform(self.matrix, self.spacing, M, slice_number, orientation, self.interp_method, self.matrix.min(), tmp_array)
                 if self._type_projection == const.PROJECTION_NORMAL:
-                    n_image = tmp_array.squeeze()
+                    n_image = tmp_array.reshape(dz, dy)
                 else:
                     if inverted:
                         tmp_array = tmp_array[:, :, ::-1]
@@ -185,12 +185,9 @@ class InnerPanel(wx.Panel):
                 slice_amont = group.nslices
         nslices_result = slice_amont / (interval + 1)
-        if (nslices_result > 1):
-            Publisher.sendMessage('Open DICOM group', group=group,
-                                  interval=interval,
-                                  file_range=(self.first_image_selection, self.last_image_selection))
-        else:
-            dlg.MissingFilesForReconstruction()
+        Publisher.sendMessage('Open DICOM group', group=group,
+                              interval=interval,
+                              file_range=(self.first_image_selection, self.last_image_selection))
 class TextPanel(wx.Panel):
     def __init__(self, parent):
@@ -264,21 +264,20 @@ class ProgressBitmapReader:
         Publisher.sendMessage("End bitmap load", data=bitmap_list)
     def GetBitmaps(self, path, recursive):
-
         y = yGetBitmaps(path, recursive)
         for value_progress in y:
+            print(">>> YYYYYY", value_progress)
             if not self.running:
                 break
             if isinstance(value_progress, tuple):
+                print("UPDATE PROGRESS")
                 self.UpdateLoadFileProgress(value_progress)
             else:
+                print("END PROGRESS")
                 self.EndLoadFile(value_progress)
-        #Is necessary in the case user cancel
-        #the load, ensure that dicomdialog is closed
-        if(self.stoped):
-            self.UpdateLoadFileProgress(None)
-            self.stoped = False   
+        self.UpdateLoadFileProgress(None)
+        self.stoped = False
 def VtkErrorPNGWriter(obj, f):
     global vtk_error