Merge branch 'invesalius:master' into context-menu-improvements

invesalius/data/imagedata_utils.py

@@ -24,7 +24,6 @@
 
 import gdcm
 import imageio
-import numpy
 import numpy as np
 
 from scipy.ndimage import shift, zoom
@@ -38,6 +37,7 @@
 import invesalius.data.converters as converters
 import invesalius.data.coordinates as dco
 import invesalius.data.slice_ as sl
+import invesalius.gui.dialogs as dlg
 import invesalius.reader.bitmap_reader as bitmap_reader
 from invesalius.i18n import tr as _
 from invesalius.data import vtk_utils as vtk_utils
@@ -158,7 +158,7 @@ def FixGantryTilt(matrix, spacing, tilt):
     Fix gantry tilt given a vtkImageData and the tilt value. Return new
     vtkImageData.
     """
-    angle = numpy.radians(tilt)
+    angle = np.radians(tilt)
     spacing = spacing[0], spacing[1], spacing[2]
     gntan = math.tan(angle)
 
@@ -308,7 +308,7 @@ def array2memmap(arr, filename=None):
     fd = None
     if filename is None:
         fd, filename = tempfile.mkstemp(prefix="inv3_", suffix=".dat")
-    matrix = numpy.memmap(filename, mode="w+", dtype=arr.dtype, shape=arr.shape)
+    matrix = np.memmap(filename, mode="w+", dtype=arr.dtype, shape=arr.shape)
     matrix[:] = arr[:]
     matrix.flush()
     if fd:
@@ -359,7 +359,7 @@ def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage
             )
 
     if resolution_percentage == 1.0:
-        matrix = numpy.memmap(temp_file, mode="w+", dtype="int16", shape=shape)
+        matrix = np.memmap(temp_file, mode="w+", dtype="int16", shape=shape)
 
     cont = 0
     max_scalar = None
@@ -394,7 +394,7 @@ def bitmap2memmap(files, slice_size, orientation, spacing, resolution_percentage
 
             if not (first_resample_entry):
                 shape = shape[0], yx_shape[0], yx_shape[1]
-                matrix = numpy.memmap(temp_file, mode="w+", dtype="int16", shape=shape)
+                matrix = np.memmap(temp_file, mode="w+", dtype="int16", shape=shape)
                 first_resample_entry = True
 
             image = image_resized
@@ -460,7 +460,7 @@ def dcm2memmap(files, slice_size, orientation, resolution_percentage):
     else:
         shape = len(files), slice_size[1], slice_size[0]
 
-    matrix = numpy.memmap(temp_file, mode="w+", dtype="int16", shape=shape)
+    matrix = np.memmap(temp_file, mode="w+", dtype="int16", shape=shape)
     for n, f in enumerate(files):
         im_array = read_dcm_slice_as_np2(f, resolution_percentage)[::-1]
 
@@ -495,7 +495,7 @@ def dcmmf2memmap(dcm_file, orientation):
     if samples_per_pixel == 3:
         np_image = image_normalize(rgb2gray(np_image), 0, 255)
     temp_fd, temp_file = tempfile.mkstemp()
-    matrix = numpy.memmap(temp_file, mode="w+", dtype="int16", shape=np_image.shape)
+    matrix = np.memmap(temp_file, mode="w+", dtype="int16", shape=np_image.shape)
     z, y, x = np_image.shape
     if orientation == "CORONAL":
         spacing = xs, zs, ys
@@ -532,18 +532,29 @@ def img2memmap(group):
     # to be rescalaed so that no negative values are created when converting to int16
     # maximum of 10000 was selected arbitrarily by testing with one MRI example
     # alternatively could test if "data.dtype == 'float64'" but maybe it is too specific
-    if numpy.ptp(data) > (2**16/2-1):
+    if np.ptp(data) > (2**16/2-1):
         data = image_normalize(data, min_=0, max_=10000, output_dtype=np.int16)
+        dlg.WarningRescalePixelValues()
+
+    # images can have pixel intensities in small float numbers which after int conversion will
+    # have to be binary (0, 1). To prevent that, rescale pixel values from 0-255
+    elif data.max() < (2**3):
+        data_temp = image_normalize(data, min_=0, max_=255, output_dtype=np.int16)
+        status = dlg.DialogRescalePixelIntensity(data.max(), np.unique(data_temp).size)
+
+        if status:
+            data = data_temp
+            # dlg.WarningRescalePixelValues()
 
     # Convert RAS+ to default InVesalius orientation ZYX
-    data = numpy.swapaxes(data, 0, 2)
-    data = numpy.fliplr(data)
+    data = np.swapaxes(data, 0, 2)
+    data = np.fliplr(data)
 
-    matrix = numpy.memmap(temp_file, mode="w+", dtype=np.int16, shape=data.shape)
+    matrix = np.memmap(temp_file, mode="w+", dtype=np.int16, shape=data.shape)
     matrix[:] = data[:]
     matrix.flush()
 
-    scalar_range = numpy.amin(matrix), numpy.amax(matrix)
+    scalar_range = np.amin(matrix), np.amax(matrix)
     os.close(temp_fd)
 
     return matrix, scalar_range, temp_file

invesalius/gui/dialogs.py

@@ -848,7 +848,20 @@ def ImportInvalidFiles(ftype="DICOM"):
     dlg.Destroy()
 
 
-def ImportAnalyzeWarning():
+def WarningRescalePixelValues():
+    msg1 = _("Warning! Pixel values are smaller than 8 (possible float values).\n")
+    msg2 = _("Pixel values have been rescaled from 0-255 for compatibility.")
+    if sys.platform == 'darwin':
+        dlg = wx.MessageDialog(None, "", msg1 + msg2,
+                                wx.ICON_INFORMATION | wx.OK)
+    else:
+        dlg = wx.MessageDialog(None, msg1 + msg2, "InVesalius 3",
+                                wx.ICON_INFORMATION | wx.OK)
+    dlg.ShowModal()
+    dlg.Destroy()
+
+
+def ImagePixelRescaling():
     msg1 = _("Warning! InVesalius has limited support to Analyze format.\n")
     msg2 = _("Slices may be wrongly oriented and functions may not work properly.")
     if sys.platform == 'darwin':
@@ -5612,6 +5625,73 @@ def Close(self):
         wx.Dialog.Close(self)
         self.Destroy()
 
+
+class SelectNiftiVolumeDialog(wx.Dialog):
+    def __init__(self, volumes, title=_(u"Select NIfTI volume")):
+        wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, title,
+                           style=wx.DEFAULT_DIALOG_STYLE | wx.FRAME_FLOAT_ON_PARENT)
+
+        self._init_gui(volumes)
+
+    def _init_gui(self, volumes):
+
+        self.cmb_volume = wx.ComboBox(self, -1, choices=volumes, style=wx.CB_DROPDOWN | wx.CB_READONLY)
+
+        button_ok = wx.Button(self, wx.ID_OK)
+        button_ok.SetHelpText("")
+        button_ok.SetDefault()
+
+        button_cancel = wx.Button(self, wx.ID_CANCEL)
+        button_cancel.SetHelpText("")
+
+        button_sizer = wx.StdDialogButtonSizer()
+        button_sizer.AddButton(button_ok)
+        button_sizer.AddButton(button_cancel)
+        button_sizer.Realize()
+
+        main_sizer = wx.BoxSizer(wx.VERTICAL)
+
+        # main_sizer.Add((5, 5))
+        # main_sizer.Add(
+            # wx.StaticText(self, -1, _("Select NIfTI volume:")), 0, wx.EXPAND, 5)
+        main_sizer.Add((5, 5))
+        main_sizer.Add(self.cmb_volume, 1, wx.EXPAND | wx.ALL, 5)
+        main_sizer.Add((5, 5))
+        main_sizer.Add(button_sizer, 0, wx.EXPAND | wx.TOP | wx.BOTTOM, 5)
+        main_sizer.Add((5, 5))
+
+        self.SetSizer(main_sizer)
+        main_sizer.Fit(self)
+        self.Layout()
+        self.CenterOnParent()
+
+    def GetVolumeChoice(self):
+        volume_choice = int(self.cmb_volume.GetString(self.cmb_volume.GetSelection())) - 1
+
+        return volume_choice
+
+
+def DialogRescalePixelIntensity(max_intensity, unique_values):
+    msg = _("Maximum pixel intensity is: ") + str(round(max_intensity, 1)) + '\n\n' + \
+          _("Number of unique pixel intensities: ") + str(unique_values) + '\n\n' + \
+          _("Would you like to rescale pixel values to 0-255?")
+
+    if sys.platform == 'darwin':
+        dlg = wx.MessageDialog(None, "", msg,
+                               wx.YES_NO)
+    else:
+        dlg = wx.MessageDialog(None, msg, "InVesalius 3",
+                               wx.YES_NO)
+
+    if dlg.ShowModal() == wx.ID_YES:
+        status = True
+    else:
+        status = False
+
+    dlg.Destroy()
+    return status
+
+
 class ConfigureOptitrackDialog(wx.Dialog):
     def __init__(self, title=_("Configure Optitrack")):
         wx.Dialog.__init__(self, wx.GetApp().GetTopWindow(), -1, title, size=wx.Size(1000, 200),

invesalius/reader/others_reader.py

@@ -50,6 +50,37 @@ def ReadOthers(dir_):
         imagedata = nib.squeeze_image(nib.load(dir_))
         imagedata = nib.as_closest_canonical(imagedata)
         imagedata.update_header()
+
+        if len(imagedata.shape) == 4:
+            import invesalius.gui.dialogs as dlg
+            from wx import ID_OK
+
+            dialog = dlg.SelectNiftiVolumeDialog(volumes=[str(n+1) for n in range(imagedata.shape[-1])])
+            status = dialog.ShowModal()
+
+            success = status == ID_OK
+
+            if success:
+                # selected_option = int(dialog.choice.GetStringSelection())
+                selected_volume = dialog.GetVolumeChoice()
+
+                data = imagedata.get_fdata()
+                header = imagedata.header.copy()
+
+                selected_volume = data[..., selected_volume]
+                header.set_data_shape(selected_volume.shape)
+
+                zooms = list(header.get_zooms())
+                new_zooms = zooms[:3]  # Adjust this to your desired zooms
+                header.set_zooms(new_zooms)
+
+                imagedata = nib.Nifti1Image(selected_volume, imagedata.affine, header=header)
+
+            else:
+                raise ValueError
+
+            dialog.Destroy()
+
     except(nib.filebasedimages.ImageFileError):
         return False