Merge pull request #71 from haesleinhuepf/slice-nd-images

haesleinhuepf · web-flow · commit 343329b5d16f · 2024-09-04T14:44:04.000+02:00
support for n-dimensional data
diff --git a/README.md b/README.md
@@ -233,6 +233,13 @@ stackview.switch(
 
 ![](https://raw.githubusercontent.com/haesleinhuepf/stackview/main/docs/images/demo_switch_toggleable.gif)
 
+### nD-Viewer
+
+You can also use all functions above with n-dimensional data (since stackview 0.11.0). You will then see multiple sliders for navigating through dimensions such as space and time.
+In case you work with multiple channels, using `stackview.switch()` with `toggleable=True` is recommended ([Read more](https://github.com/haesleinhuepf/stackview/blob/main/docs/nd-data.ipynb)).
+
+![](https://raw.githubusercontent.com/haesleinhuepf/stackview/main/docs/images/nd-data.gif)
+
 
 ### Crop
 
diff --git a/docs/data/mitosis.tif b/docs/data/mitosis.tif
diff --git a/docs/demo.ipynb b/docs/demo.ipynb
diff --git a/docs/images/nd-data.gif b/docs/images/nd-data.gif
diff --git a/docs/nd-data.ipynb b/docs/nd-data.ipynb
diff --git a/stackview/__init__.py b/stackview/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.9.2"
+__version__ = "0.10.0"
 
 from ._static_view import jupyter_displayable_output, insight
 from ._utilities import merge_rgb
diff --git a/stackview/_annotate.py b/stackview/_annotate.py
@@ -43,7 +43,7 @@ def annotate(
     slice_number : int, optional
         Slice-position in the stack
     axis: int, optional
-        Axis where the slice-position can be modified interactively
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     alpha : float, optional
         Alpha blending value for the labels on top of the image
     continuous_update : bool, optional
diff --git a/stackview/_crop.py b/stackview/_crop.py
@@ -21,7 +21,7 @@ def crop(image,
     slice_number : int, optional
         Slice-position in the stack to be shown (default: center plane)
     axis : int, optional
-        Axis along which we slice the shown stack (default: 0)
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     continuous_update : bool, optional
         Update the image while dragging the sliders, default: False
     slider_text: str, optional
diff --git a/stackview/_curtain.py b/stackview/_curtain.py
@@ -28,7 +28,7 @@ def curtain(
     slice_number : int, optional
         Slice-position in case we are looking at an image stack
     axis : int, optional
-        Axis in case we are slicing a stack
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     display_width : int, optional
         This parameter is obsolete. Use zoom_factor instead
     display_height : int, optional
diff --git a/stackview/_display_range.py b/stackview/_display_range.py
@@ -19,7 +19,7 @@ def display_range(
     slice_number : int, optional
         Slice-position in case we are looking at an image stack
     axis : int, optional
-        Axis in case we are slicing a stack
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     display_width : int, optional
         This parameter is obsolete. Use zoom_factor instead
     display_height : int, optional
diff --git a/stackview/_imshow.py b/stackview/_imshow.py
@@ -63,7 +63,7 @@ def imshow(image,
         warnings.warn("The parameter max_display_intensity is deprecated, use max_display_intensity instead.")
         max_display_intensity = vmax
 
-    if len(image.shape) == 3 and image.shape[-1] > 4:
+    while len(image.shape) > 2 and image.shape[-1] not in [3, 4]: #[3,4]: RGB, RGBA
         image = image.max(axis=0)
 
     if 'cupy.ndarray' in str(type(image)):
diff --git a/stackview/_orthogonal.py b/stackview/_orthogonal.py
@@ -48,9 +48,9 @@ def orthogonal(
         image = image.get()
 
     widgets = [
-        slice(image, axis=0, slider_text="Z", continuous_update=continuous_update, zoom_factor=zoom_factor, zoom_spline_order=zoom_spline_order, colormap=colormap, display_min=display_min, display_max=display_max),
-        slice(image, axis=1, slider_text="Y", continuous_update=continuous_update, zoom_factor=zoom_factor, zoom_spline_order=zoom_spline_order, colormap=colormap, display_min=display_min, display_max=display_max),
-        slice(image, axis=2, slider_text="X", continuous_update=continuous_update, zoom_factor=zoom_factor, zoom_spline_order=zoom_spline_order, colormap=colormap, display_min=display_min, display_max=display_max),
+        slice(image, slider_text="Z", continuous_update=continuous_update, zoom_factor=zoom_factor, zoom_spline_order=zoom_spline_order, colormap=colormap, display_min=display_min, display_max=display_max),
+        slice(image.swapaxes(-3,-2).swapaxes(-2,-1), slider_text="Y", continuous_update=continuous_update, zoom_factor=zoom_factor, zoom_spline_order=zoom_spline_order, colormap=colormap, display_min=display_min, display_max=display_max),
+        slice(image.swapaxes(-3,-1), slider_text="X", continuous_update=continuous_update, zoom_factor=zoom_factor, zoom_spline_order=zoom_spline_order, colormap=colormap, display_min=display_min, display_max=display_max),
     ]
 
     def update(event=None):
diff --git a/stackview/_side_by_side.py b/stackview/_side_by_side.py
@@ -27,7 +27,7 @@ def side_by_side(
     slice_number : int, optional
         Slice-position in the stack
     axis : int, optional
-        Axis in case we are slicing a stack
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     display_width : int, optional
         This parameter is obsolete. Use zoom_factor instead
     display_height : int, optional
diff --git a/stackview/_slice.py b/stackview/_slice.py
@@ -5,7 +5,7 @@ def slice(
         display_width : int = None,
         display_height : int = None,
         continuous_update:bool = True,
-        slider_text:str="Slice",
+        slider_text:str="[{}]",
         zoom_factor:float = 1.0,
         zoom_spline_order:int = 0,
         colormap:str = None,
@@ -21,13 +21,15 @@ def slice(
     slice_number : int, optional
         Slice-position in the stack
     axis : int, optional
-        Axis in case we are slicing a stack
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     display_width : int, optional
         This parameter is obsolete. Use zoom_factor instead
     display_height : int, optional
         This parameter is obsolete. Use zoom_factor instead
     continuous_update : bool, optional
         Update the image while dragging the mouse, default: False
+    slider_text: list or str, optional
+        Text shown next to the slider(s).
     zoom_factor: float, optional
         Allows showing the image larger (> 1) or smaller (<1)
     zoom_spline_order: int, optional
diff --git a/stackview/_slice_viewer.py b/stackview/_slice_viewer.py
@@ -10,7 +10,7 @@ def __init__(self,
                  display_width: int = None,
                  display_height: int = None,
                  continuous_update: bool = True,
-                 slider_text: str = "Slice",
+                 slider_text: str = "[{}]",
                  zoom_factor:float = 1.0,
                  zoom_spline_order:int = 0,
                  colormap:str = None,
@@ -21,43 +21,54 @@ def __init__(self,
         from ._image_widget import ImageWidget
 
         self.image = image
-        self.axis = axis
+        #self.axis = axis
 
         if slice_number is None:
-            slice_number = int(image.shape[axis] / 2)
+            slice_number = [int(s / 2) for s in image.shape[:-2]]
+        if isinstance(slice_number, int):
+            slice_number = [slice_number] * (len(image.shape) - 2)
+        if not isinstance(slider_text, list):
+            slider_text = [slider_text] * (len(image.shape) - 2)
 
-        if len(self.image.shape) > 2: # and self.image.shape[-1] != 3:
-            sliced_image = np.take(image, slice_number, axis=axis)
-        else:
-            sliced_image = image
-        self.view = ImageWidget(sliced_image,
+        self.sliders = []
+        offset = 2
+        if 3 >= image.shape[-1] >= 4: # RGB or RGBA images
+            offset = 3
+        for d in range(len(image.shape) - offset):
+            slider = ipywidgets.IntSlider(
+                value=slice_number[d],
+                min=0,
+                max=image.shape[d] - 1,
+                continuous_update=continuous_update,
+                description=slider_text[d].format(d),
+            )
+            slider.observe(self.update)
+            self.sliders.append(slider)
+
+        self.view = ImageWidget(self.get_view_slice(),
                                 zoom_factor=zoom_factor,
                                 zoom_spline_order=zoom_spline_order,
                                 colormap=colormap,
                                 display_min=display_min,
                                 display_max=display_max)
 
         # setup user interface for changing the slice
-        self.slice_slider = ipywidgets.IntSlider(
-            value=slice_number,
-            min=0,
-            max=image.shape[axis] - 1,
-            continuous_update=continuous_update,
-            description=slider_text,
-        )
+        self.slice_slider = ipywidgets.VBox(self.sliders[::-1])
         # widgets.link((sliders1, 'value'), (slider2, 'value'))
 
         # connect user interface with event
-        self.slice_slider.observe(self.update)
+        #self.slice_slider.observe(self.update)
 
         self.update()
 
     # event handler when the user changed something:
     def update(self, event=None):
-        if len(self.image.shape) == 3 and self.image.shape[-1] != 3:
+        self.view.data = self.get_view_slice()
+        return
+        if len(self.image.shape) == 3 and self.image.shape[-1] != 3: # 3D
             self.slice_slider.layout.display = None
             self.view.data = np.take(self.image, self.slice_slider.value, axis=self.axis)
-        elif len(self.image.shape) == 4 and self.image.shape[-1] == 3:
+        elif len(self.image.shape) == 4 and self.image.shape[-1] == 3: # 3D RGB
             self.slice_slider.layout.display = None
             self.view.data = np.take(self.image, self.slice_slider.value, axis=self.axis)
         elif len(self.image.shape) == 4:
@@ -69,3 +80,9 @@ def update(self, event=None):
     def configuration_updated(self, event=None):
         warnings.warn('SliceViewer.configuration_updated is deprecated, use SliceViewer.update instead.')
         return self.update(event)
+
+    def get_view_slice(self):
+        data = self.image
+        for d, slider in enumerate(self.sliders):
+            data = np.take(data, slider.value, axis=0)
+        return data
diff --git a/stackview/_static_view.py b/stackview/_static_view.py
@@ -70,7 +70,8 @@ def _repr_html_(self):
         labels = _is_label_image(self.obj)
 
         import matplotlib.pyplot as plt
-        _imshow(self.obj,
+        from ._imshow import imshow
+        imshow(self.obj,
                 labels=labels,
                 continue_drawing=True,
                 colorbar=not labels)
diff --git a/stackview/_switch.py b/stackview/_switch.py
@@ -4,7 +4,7 @@ def switch(images,
            display_width : int = None,
            display_height : int = None,
            continuous_update:bool = True,
-           slider_text:str="Slice",
+           slider_text:str="[{}]",
            zoom_factor:float = 1.0,
            zoom_spline_order:int = 0,
            colormap:str = None,
@@ -21,7 +21,7 @@ def switch(images,
     slice_number : int, optional
         Slice-position in the stack
     axis : int, optional
-        Axis in case we are slicing a stack
+        This parameter is obsolete. If you want to show any other axis than the first, you need to transpose the image before, e.g. using np.swapaxes().
     display_width : int, optional
         This parameter is obsolete. Use zoom_factor instead
     display_height : int, optional
@@ -90,14 +90,11 @@ def switch(images,
 
     if toggleable:
         def display_(buttons, images, colormap, display_min, display_max):
-            display_image = np.zeros(list(images[0].shape) + [3])
+            display_image = None
             for button, image, colormap_, display_min_, display_max_ in zip(buttons, images, colormap,
                                                                              display_min, display_max):
                 if button.value:
-                    if len(image.shape) == 3 and image.shape[-1] != 3:
-                        display_image_to_add = np.asarray([_img_to_rgb(i, display_min=display_min_, display_max=display_max_, colormap=colormap_) for i in image])
-                    else:
-                        display_image_to_add = _img_to_rgb(image, display_min=display_min_, display_max=display_max_, colormap=colormap_)
+                    display_image_to_add = _image_stack_to_rgb(image, display_min=display_min_, display_max=display_max_, colormap=colormap_)
                         
                     if display_image is None:
                         display_image = display_image_to_add
@@ -161,3 +158,15 @@ def act(event=None):
 
     button.observe(act, 'value')
     return button
+
+def _image_stack_to_rgb(image, display_min, display_max, colormap):
+    import numpy as np
+    from ._image_widget import _img_to_rgb
+
+    dims = list(image.shape)
+    if 3 <= dims[-1] <= 4:
+        dims = dims[:-1]
+
+    if len(dims) > 2:
+        return np.asarray([_image_stack_to_rgb(i, display_min=display_min, display_max=display_max, colormap=colormap) for i in image])
+    return _img_to_rgb(image, display_min=display_min, display_max=display_max, colormap=colormap)

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-__version__ = "0.9.2"`
	`1`	`+__version__ = "0.10.0"`
`2`	`2`
`3`	`3`	`from ._static_view import jupyter_displayable_output, insight`
`4`	`4`	`from ._utilities import merge_rgb`