[#46] handle colored images

config/default.json

@@ -1,11 +1,11 @@
 {
     "window_size": [
-        958,
-        1003
+        1920,
+        1013
     ],
     "window_position": [
-        960,
-        0
+        -48,
+        39
     ],
     "module_width": 250,
     "space_between_modules": [
@@ -32,7 +32,7 @@
     "style": "Default",
     "theme": "bright",
     "filenames": [
-        "C:\\Users\\jean\\Desktop\\francis\\resources\\data\\out\\# not saved"
+        "C:/Users/jean/Desktop/francis/resources/data/out\\graph_27062021 15h22m54.iag"
     ],
     "current_tab": 0
 }

src/model/model.py

@@ -40,7 +40,7 @@ def load(self, path):
         elif ext == '.nii' or path.endswith('.nii.gz'):
             data = nib.load(path).get_fdata()
         elif ext in ['.png', '.jpg']:
-            data = imageio.imread(path, as_gray=True)
+            data = imageio.imread(path)
         else:
             raise TypeError("{} not handle yet".format(ext))
         return data
@@ -71,15 +71,22 @@ def save(self, data, path):
             ni_img = nib.Nifti1Image(data, None)
             nib.save(ni_img, path)
         elif ext in ['.png', '.jpg']:
-            # 3D image can be saved as a list of 2D images in a directory
-            if len(data.shape) == 3:
+            data = np.squeeze(data)
+            if data.ndim == 3 and np.min(data.shape) < 5:
+                # save 3d image as rgb or rgba image if possible
+                # (smaller dimension send to the end)
+                data = np.rollaxis(data, np.argmin(data.shape), data.ndim)
+            elif data.ndim > 2:
+                # 3D image can be saved as a list of 2D images in a directory
+                # work for ndimage recursively
                 if not os.path.exists(root):
                     os.makedirs(root)
                 head, tail = os.path.split(root)
                 for i in range(data.shape[0]):
                     new_path = os.path.join(root, tail+str(i)+ext)
                     self.save(data[i], new_path)
                 return "images are saved in directory {}".format(root)
+
             imageio.imwrite(path, data)
         return "saved as {}".format(path)
 

src/presenter/presenter.py

@@ -226,7 +226,7 @@ def browse_path(self, module):
             module.parameters.path.setToolTip(filename)
 
     # ----------------------------- MODEL CALL --------------------------------#
-    @utils.manager(1)
+    @utils.manager(2)
     def call_save(self, module):
         """
         save the parent image as nifti file at specified path
@@ -237,7 +237,7 @@ def call_save(self, module):
                 "path": module.parameters.path.text()}
         return function, args
 
-    @utils.manager(1)
+    @utils.manager(2)
     def call_load(self, module):
         """
         load any type of data
@@ -246,7 +246,7 @@ def call_load(self, module):
         args = {"path": module.parameters.path.text()}
         return function, args
 
-    @utils.manager(1)
+    @utils.manager(2)
     def call_get_img_infos(self, module):
         """
         get image info
@@ -258,7 +258,7 @@ def call_get_img_infos(self, module):
                 "info": module.parameters.infos.currentText()}
         return function, args
 
-    @utils.manager(1)
+    @utils.manager(2)
     def call_apply_threshold(self, module):
         """
         compute 3d thresholding on the parent image
@@ -272,7 +272,7 @@ def call_apply_threshold(self, module):
                 "reverse": module.parameters.reversed.isChecked()}
         return function, args
 
-    @utils.manager(1)
+    @utils.manager(2)
     def call_apply_operation(self, module):
         """
         compute operations between multiple images
@@ -287,7 +287,7 @@ def call_apply_operation(self, module):
                 "operation": utils.get_checked(module.parameters, ['add', 'multiply', 'subtract', 'divide'])}
         return function, args
 
-    @utils.manager(1)
+    @utils.manager(2)
     def call_apply_simple_operation(self, module):
         """
         compute simple operations between an image and a float
@@ -300,7 +300,7 @@ def call_apply_simple_operation(self, module):
                 "operation": utils.get_checked(module.parameters, ['add', 'multiply', 'subtract', 'divide'])}
         return function, args
 
-    @utils.manager(1)
+    @utils.manager(2)
     def call_apply_basic_morpho(self, module):
         """
         compute 3d morphological operation on the parent image

src/view/graph_bricks.py

@@ -405,22 +405,28 @@ def snapMousePressEvent(self, event):
         # set ratio between image and qpixmap
         im = self.graph.resultStack.get(self.name)
         if im is not None:
-            if len(im.shape) == 2:
-                ratio = im.shape[1] / self.result.width()
-            else:
+            if self.result.slicable:
                 ratio = im.shape[int(self.result.axis == 0)] / self.result.width()
+            else:
+                ratio = im.shape[1] / self.result.width()
+
             # get click position
             click_pos = np.array([event.pos().y(), event.pos().x()])
             # define position in image
             true_pos = np.rint(click_pos * ratio).astype(int)
             try:
-                if len(im.shape) == 2:
+                if im.ndim == 2:
                     x, y, z = *true_pos, ''
+                    value = im[x, y]
                     self.rightfoot.setText("%d " % im[x, y])
-                else:
+                elif self.result.slicable:
                     x, y, z = np.insert(true_pos, self.result.axis, self.result.currentSlice)
-                    self.rightfoot.setText("%d " % im[x, y, z])
+                    value = im[x, y, z]
+                else:
+                    x, y, z = *true_pos, ''
+                    value = "(" + " ".join(im[x, y].astype(str)) + ")"
                 self.leftfoot.setText("{0} {1} {2}".format(x, y, z))
+                self.rightfoot.setText(str(value))
             except IndexError as e:
                 # click outside image
                 print(e)

src/view/ui.py

@@ -189,10 +189,9 @@ class QImageRenderer(QtWidgets.QLabel):
     def __init__(self, img, parent):
         QtWidgets.QWidget.__init__(self)
         self.img = self.formatImage(img)
-        self.dimension = len(self.img.shape)
-        if self.dimension == 3:
-            self.axis = 0
-            self.currentSlice = None
+
+        self.getImageType()
+
         self.pixmap = None
         self._parent = parent
         self.updateSnap()
@@ -216,7 +215,7 @@ def formatImage(self, img):
         return img
 
     def wheelEvent(self, event):
-        if self.dimension != 3:
+        if not self.slicable:
             return
         if self.currentSlice is not None:
             step = 1
@@ -231,7 +230,7 @@ def mouseDoubleClickEvent(self, event):
         """
         update image axis on double click above image view
         """
-        if self.dimension != 3:
+        if not self.slicable:
             return
         if self.axis == 2:
             self.axis = 0
@@ -240,37 +239,54 @@ def mouseDoubleClickEvent(self, event):
         self.updateSnap()
         self.syncSignal.emit()
 
+    def getImageType(self):
+        self.slicable = False
+        self.imgType = QtGui.QImage.Format_Grayscale8
+        if self.img.ndim == 3:
+            if self.img.shape[-1] == 3:
+                self.imgType = QtGui.QImage.Format_RGB888
+            elif self.img.shape[-1] == 4:
+                self.imgType = QtGui.QImage.Format_RGBA8888
+            else:
+                self.slicable = True
+
+        if self.slicable:
+            self.axis = 0
+            self.currentSlice = None
+
     def getSliceParams(self):
-        if self.dimension == 2:
-            return self.img, self.img.shape[1], self.img.shape[0]
-        elif self.dimension == 3:
-            s = self.img.shape[self.axis]
-
-            # set current slice
-            if self.currentSlice is None:
-                self.currentSlice = int(s / 2)
-            elif self.currentSlice < 0:
-                self.currentSlice = 0
-            elif self.currentSlice >= s:
-                self.currentSlice = s-1
-
-            # snap axis slice
-            if self.axis == 0:
-                im_slice = self.img[self.currentSlice].copy()
-                _, h, w = self.img.shape
-            elif self.axis == 1:
-                im_slice = self.img[:, self.currentSlice].copy()
-                h, _, w = self.img.shape
-            elif self.axis == 2:
-                im_slice = self.img[:, :, self.currentSlice].copy()
-                h, w, _ = self.img.shape
-
-            return im_slice, w, h
+        if self.img.ndim == 2:
+            return self.img, self.img.shape[1], self.img.shape[0], self.img.shape[1]
+        elif self.img.ndim == 3:
+            if not self.slicable:
+                return self.img, self.img.shape[1], self.img.shape[0], self.img.shape[1] * self.img.shape[2]
+            else:
+                s = self.img.shape[self.axis]
+
+                # set current slice
+                if self.currentSlice is None:
+                    self.currentSlice = int(s / 2)
+                elif self.currentSlice < 0:
+                    self.currentSlice = 0
+                elif self.currentSlice >= s:
+                    self.currentSlice = s-1
+
+                # snap axis slice
+                if self.axis == 0:
+                    im_slice = self.img[self.currentSlice].copy()
+                    _, h, w = self.img.shape
+                elif self.axis == 1:
+                    im_slice = self.img[:, self.currentSlice].copy()
+                    h, _, w = self.img.shape
+                elif self.axis == 2:
+                    im_slice = self.img[:, :, self.currentSlice].copy()
+                    h, w, _ = self.img.shape
+
+                return im_slice, w, h, w
 
     def updateSnap(self):
-        im, w, h = self.getSliceParams()
-        qim = QtGui.QImage(im, w, h, w, QtGui.QImage.Format_Indexed8)
-        qim.setColorTable([QtGui.qRgba(255, 0, 0, 255)]+[QtGui.qRgba(i, i, i, 255) for i in range(1, 256)])
+        im, w, h, bytesPerLine = self.getSliceParams()
+        qim = QtGui.QImage(im, w, h, bytesPerLine, self.imgType)
         self.pixmap = QtGui.QPixmap(qim)
         self.pixmap = self.pixmap.scaledToWidth(self._parent.width() - 2,
                                                 QtCore.Qt.FastTransformation)