pumpia 0.1.0__py3-none-any.whl

pumpia/contrib/example/collection.py

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+from pumpia.contrib.example.module import ExampleModule
+from pumpia.module_handling.module_collections import (BaseCollection,
+                                                       OutputFrame,
+                                                       WindowGroup)
+from pumpia.module_handling.in_outs.viewer_ios import ArrayViewerIO
+from pumpia.module_handling.in_outs.groups import IOGroup
+from pumpia.widgets.viewers import BaseViewer
+from pumpia.image_handling.image_structures import ImageCollection
+from pumpia.utilities.tkinter_utils import tk_copy
+
+
+class ExampleCollection(BaseCollection):
+    """
+    An example collection.
+
+    This collection demonstrates the use of the PumpIA collections.
+    It has 2 viewers in the main window and loads 2 `ExampleModule` instances into a second window.
+    """
+    viewer1 = ArrayViewerIO(row=0, column=0)
+    viewer2 = ArrayViewerIO(row=0, column=1, main=True)
+
+    module1 = ExampleModule()
+    module2 = ExampleModule()
+
+    average_output = OutputFrame()
+
+    # makes sure the two modules are in the same window in the collection
+    group = WindowGroup([module1, module2])
+
+    def load_outputs(self):
+        self.average_output.register_output(self.module1.average, verbose_name="Average 1")
+        self.average_output.register_output(self.module2.average, verbose_name="Average 2")
+        IOGroup([self.module1.size, self.module2.size])
+
+    def on_image_load(self, viewer: BaseViewer) -> None:
+        # loads the image loaded into a viewer into the relevant modules viewer
+        # if the image is an ImageCollection then only loads the first image into the module
+        if viewer is self.viewer1:
+            if self.viewer1.image is not None:
+                image = self.viewer1.image
+                if isinstance(image, ImageCollection):
+                    self.module1.viewer.load_image(image.image_set[0])
+                else:
+                    self.module1.viewer.load_image(image)
+
+        elif viewer is self.viewer2:
+            if self.viewer2.image is not None:
+                image = self.viewer2.image
+                if isinstance(image, ImageCollection):
+                    self.module2.viewer.load_image(image.image_set[0])
+                else:
+                    self.module2.viewer.load_image(image)
+
+    def load_commands(self):
+        self.register_command("Copy Averages", self.copy_averages)
+
+    def copy_averages(self):
+        """
+        Copy the values of the averages to the clipboard, comma seperated.
+        """
+        tk_copy(", ".join([str(self.module1.average.value), str(self.module2.average.value)]))

pumpia/contrib/example/example.py

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+"""
+Example
+"""
+import math
+
+from pumpia.module_handling.modules import BaseModule
+from pumpia.module_handling.module_collections import (BaseCollection,
+                                                       OutputFrame,
+                                                       WindowGroup)
+from pumpia.module_handling.in_outs.roi_ios import BaseInputROI, InputEllipseROI
+from pumpia.module_handling.in_outs.viewer_ios import ArrayViewerIO
+from pumpia.module_handling.in_outs.simple import PercInput, FloatOutput, IntOutput
+from pumpia.module_handling.in_outs.groups import IOGroup
+from pumpia.module_handling.context import SimpleContext
+from pumpia.widgets.viewers import BaseViewer
+from pumpia.image_handling.roi_structures import EllipseROI
+from pumpia.image_handling.image_structures import ImageCollection
+from pumpia.utilities.tkinter_utils import tk_copy
+
+
+class ExampleModule(BaseModule):
+    """
+    An Example Module.
+
+    This module demonstrates the use of the PumpIA modules.
+    It draws an ellipse ROI on an image based on the size of image and input from the user.
+    The analysis calculates the average pixel value within the ellipse,
+    or the root sum of squares of the means if a multisample image.
+    """
+    viewer = ArrayViewerIO(row=0, column=0)
+    size = PercInput(80, verbose_name="Size (%)")
+    ellipse_roi = InputEllipseROI("Ellipse ROI")
+
+    width = IntOutput(verbose_name="Width (px)")
+    height = IntOutput(verbose_name="Height (px)")
+    average = FloatOutput()
+
+    def link_rois_viewers(self):
+        self.ellipse_roi.viewer = self.viewer
+
+    def draw_rois(self, context: SimpleContext, batch: bool = False):
+        if self.viewer.image is not None:
+            factor = self.size.value / 100
+            a = round(factor * context.width / 2)
+            b = round(factor * context.height / 2)
+            self.ellipse_roi.register_roi(EllipseROI(self.viewer.image,
+                                                     round(context.xcent),
+                                                     round(context.ycent),
+                                                     a,
+                                                     b,
+                                                     slice_num=self.viewer.current_slice))
+
+    def post_roi_register(self, roi_input: BaseInputROI):
+        if self.ellipse_roi.roi is not None and self.manager is not None:
+            self.manager.add_roi(self.ellipse_roi.roi)
+
+    def analyse(self, batch: bool = False):
+        if self.ellipse_roi.roi is not None:
+            roi = self.ellipse_roi.roi
+            mean = roi.mean
+            if isinstance(mean, (float, int)):
+                self.average.value = mean
+            else:
+                self.average.value = math.sqrt(math.sumprod(mean, mean))
+
+    def on_image_load(self, viewer: BaseViewer) -> None:
+        if viewer is self.viewer:
+            image = self.viewer.image
+            if image is not None:
+                self.height.value = image.shape[1]
+                self.width.value = image.shape[2]
+
+    def load_commands(self):
+        self.register_command("Copy Average", self.copy_average)
+
+    def copy_average(self):
+        """
+        Copy the value of the average to the clipboard.
+        """
+        tk_copy(str(self.average.value))
+
+
+class ExampleCollection(BaseCollection):
+    """
+    An example collection.
+
+    This collection demonstrates the use of the PumpIA collections.
+    It has 2 viewers in the main window and loads 2 `ExampleModule` instances into a second window.
+    """
+    viewer1 = ArrayViewerIO(row=0, column=0)
+    viewer2 = ArrayViewerIO(row=0, column=1, main=True)
+
+    module1 = ExampleModule()
+    module2 = ExampleModule()
+
+    average_output = OutputFrame()
+
+    # makes sure the two modules are in the same window in the collection
+    group = WindowGroup([module1, module2])
+
+    def load_outputs(self):
+        self.average_output.register_output(self.module1.average, verbose_name="Average 1")
+        self.average_output.register_output(self.module2.average, verbose_name="Average 2")
+        IOGroup([self.module1.size, self.module2.size])
+
+    def on_image_load(self, viewer: BaseViewer) -> None:
+        # loads the image loaded into a viewer into the relevant modules viewer
+        # if the image is an ImageCollection then only loads the first image into the module
+        if viewer is self.viewer1:
+            if self.viewer1.image is not None:
+                image = self.viewer1.image
+                if isinstance(image, ImageCollection):
+                    self.module1.viewer.load_image(image.image_set[0])
+                else:
+                    self.module1.viewer.load_image(image)
+
+        elif viewer is self.viewer2:
+            if self.viewer2.image is not None:
+                image = self.viewer2.image
+                if isinstance(image, ImageCollection):
+                    self.module2.viewer.load_image(image.image_set[0])
+                else:
+                    self.module2.viewer.load_image(image)
+
+    def load_commands(self):
+        self.register_command("Copy Averages", self.copy_averages)
+
+    def copy_averages(self):
+        """
+        Copy the values of the averages to the clipboard, comma seperated.
+        """
+        tk_copy(", ".join([str(self.module1.average.value), str(self.module2.average.value)]))
+
+
+if __name__ == "__main__":
+    ExampleCollection.run()

pumpia/contrib/example/module.py

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+import math
+
+from pumpia.widgets.viewers import BaseViewer
+from pumpia.module_handling.modules import BaseModule
+from pumpia.module_handling.in_outs.roi_ios import BaseInputROI, InputEllipseROI
+from pumpia.module_handling.in_outs.viewer_ios import ArrayViewerIO
+from pumpia.module_handling.in_outs.simple import PercInput, FloatOutput, IntOutput
+from pumpia.module_handling.context import SimpleContext
+from pumpia.image_handling.roi_structures import EllipseROI
+from pumpia.utilities.tkinter_utils import tk_copy
+
+
+class ExampleModule(BaseModule):
+    """
+    An Example Module.
+
+    This module demonstrates the use of the PumpIA modules.
+    It draws an ellipse ROI on an image based on the size of image and input from the user.
+    The analysis calculates the average pixel value within the ellipse,
+    or the root sum of squares of the means if a multisample image.
+    """
+    viewer = ArrayViewerIO(row=0, column=0)
+    size = PercInput(80, verbose_name="Size (%)")
+    ellipse_roi = InputEllipseROI("Ellipse ROI")
+
+    width = IntOutput(verbose_name="Width (px)")
+    height = IntOutput(verbose_name="Height (px)")
+    average = FloatOutput()
+
+    def link_rois_viewers(self):
+        self.ellipse_roi.viewer = self.viewer
+
+    def draw_rois(self, context: SimpleContext, batch: bool = False):
+        if self.viewer.image is not None:
+            factor = self.size.value / 100
+            a = round(factor * context.width / 2)
+            b = round(factor * context.height / 2)
+            self.ellipse_roi.register_roi(EllipseROI(self.viewer.image,
+                                                     round(context.xcent),
+                                                     round(context.ycent),
+                                                     a,
+                                                     b,
+                                                     slice_num=self.viewer.current_slice))
+
+    def post_roi_register(self, roi_input: BaseInputROI):
+        if self.ellipse_roi.roi is not None and self.manager is not None:
+            self.manager.add_roi(self.ellipse_roi.roi)
+
+    def analyse(self, batch: bool = False):
+        if self.ellipse_roi.roi is not None:
+            roi = self.ellipse_roi.roi
+            mean = roi.mean
+            if isinstance(mean, (float, int)):
+                self.average.value = mean
+            else:
+                self.average.value = math.sqrt(math.sumprod(mean, mean))
+
+    def on_image_load(self, viewer: BaseViewer) -> None:
+        if viewer is self.viewer:
+            image = self.viewer.image
+            if image is not None:
+                self.height.value = image.shape[1]
+                self.width.value = image.shape[2]
+
+    def load_commands(self):
+        self.register_command("Copy Average", self.copy_average)
+
+    def copy_average(self):
+        """
+        Copy the value of the average to the clipboard.
+        """
+        tk_copy(str(self.average.value))