Merge pull request #38 from zoccoler/add_example_stack

Add example stack

MANIFEST.in

@@ -4,3 +4,4 @@ include README.md
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 include src/napari_flim_phasor_plotter/data/*
+include src/napari_flim_phasor_plotter/data/hazelnut_FLIM_z_stack/*

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = napari-flim-phasor-plotter
-version = 0.0.4
+version = 0.0.5
 description = A plugin that performs phasor plot from TCSPC FLIM data.
 long_description = file: README.md
 long_description_content_type = text/markdown

src/napari_flim_phasor_plotter/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.0.4"
+__version__ = "0.0.5"
 
 from ._reader import napari_get_reader
 from ._sample_data import load_seminal_receptacle_image, load_hazelnut_image, load_hazelnut_z_stack, load_lifetime_cat_synthtetic_single_image

src/napari_flim_phasor_plotter/_plotting.py

@@ -3,47 +3,6 @@
 import numpy as np
 
 
-def add_phasor_circle(ax):
-    '''
-    Generate FLIM universal semi-circle plot
-    '''
-    import numpy as np
-    angles = np.linspace(0, np.pi, 180)
-    x = (np.cos(angles) + 1) / 2
-    y = np.sin(angles) / 2
-    ax.plot(x, y, 'yellow', alpha=0.3)
-    return ax
-
-
-def add_tau_lines(ax, tau_list, frequency):
-    import numpy as np
-    if not isinstance(tau_list, list):
-        tau_list = [tau_list]
-    frequency = frequency * 1E6  # MHz to Hz
-    w = 2 * np.pi * frequency  # Hz to radians/s
-    for tau in tau_list:
-        tau = tau * 1E-9  # nanoseconds to seconds
-        g = 1 / (1 + ((w * tau)**2))
-        s = (w * tau) / (1 + ((w * tau)**2))
-        dot, = ax.plot(g, s, marker='o', mfc='none')
-        array = np.linspace(0, g, 50)
-        y = (array * s / g)
-        ax.plot(array, y, color=dot.get_color())
-
-
-def add_2d_histogram(ax, x, y):
-    import matplotlib.pyplot as plt
-    output = ax.hist2d(
-        x=x,
-        y=y,
-        bins=10,
-        cmap='jet',
-        norm='log',
-        alpha=0.5
-    )
-    return ax
-
-
 class PhasorPlotterWidget(PlotterWidget):
     def __init__(self, napari_viewer):
         super().__init__(napari_viewer)
@@ -54,21 +13,67 @@ def run(self,
             plot_x_axis_name,
             plot_y_axis_name,
             plot_cluster_name=None,
-            redraw_cluster_image=True,):
+            redraw_cluster_image=True,
+            ):
         super().run(features=features,
                     plot_x_axis_name=plot_x_axis_name,
                     plot_y_axis_name=plot_y_axis_name,
                     plot_cluster_name=plot_cluster_name,
                     redraw_cluster_image=redraw_cluster_image,)
-        add_phasor_circle(self.graphics_widget.axes)
+
+        self.redefine_axes_limits(ensure_full_semi_circle_displayed=False)
+
+
+    def redefine_axes_limits(self, ensure_full_semi_circle_displayed=True):
         # Redefine axes limits
-        self.graphics_widget.axes.autoscale()
-        current_ylim = self.graphics_widget.axes.get_ylim()
-        current_xlim = self.graphics_widget.axes.get_xlim()
-        ylim_0 = np.amin([current_ylim[0] - 0.1 * current_ylim[0], -0.1])
-        ylim_1 = np.amax([current_ylim[1] + 0.1 * current_ylim[1], 0.7])
-        xlim_0 = np.amin([current_xlim[0] - 0.1 * current_xlim[0], -0.1])
-        xlim_1 = np.amax([current_xlim[1] + 0.1 * current_xlim[1], 1.1])
+        if ensure_full_semi_circle_displayed:
+            self.add_phasor_circle(self.graphics_widget.axes)
+            self.graphics_widget.axes.autoscale()
+            self.graphics_widget.draw()
+            current_ylim = self.graphics_widget.axes.get_ylim()
+            current_xlim = self.graphics_widget.axes.get_xlim()
+            ylim_0 = np.amin([current_ylim[0] - 0.1 * current_ylim[0], -0.1])
+            ylim_1 = np.amax([current_ylim[1] + 0.1 * current_ylim[1], 0.7])
+            xlim_0 = np.amin([current_xlim[0] - 0.1 * current_xlim[0], -0.1])
+            xlim_1 = np.amax([current_xlim[1] + 0.1 * current_xlim[1], 1.1])
+        else:
+            self.graphics_widget.axes.autoscale()
+            self.graphics_widget.draw()
+            current_ylim = self.graphics_widget.axes.get_ylim()
+            current_xlim = self.graphics_widget.axes.get_xlim()
+            self.add_phasor_circle(self.graphics_widget.axes)
+            ylim_0 = current_ylim[0] - 0.1 * current_ylim[0]
+            ylim_1 = current_ylim[1] + 0.1 * current_ylim[1]
+            xlim_0 = current_xlim[0] - 0.1 * current_xlim[0]
+            xlim_1 = current_xlim[1] + 0.1 * current_xlim[1]
         self.graphics_widget.axes.set_ylim([ylim_0, ylim_1])
         self.graphics_widget.axes.set_xlim([xlim_0, xlim_1])
         self.graphics_widget.draw_idle()
+
+
+    def add_phasor_circle(self, ax):
+        '''
+        Generate FLIM universal semi-circle plot
+        '''
+        import numpy as np
+        angles = np.linspace(0, np.pi, 180)
+        x = (np.cos(angles) + 1) / 2
+        y = np.sin(angles) / 2
+        ax.plot(x, y, 'white', alpha=0.3)
+        return ax
+
+
+    def add_tau_lines(self, ax, tau_list, frequency):
+        import numpy as np
+        if not isinstance(tau_list, list):
+            tau_list = [tau_list]
+        frequency = frequency * 1E6  # MHz to Hz
+        w = 2 * np.pi * frequency  # Hz to radians/s
+        for tau in tau_list:
+            tau = tau * 1E-9  # nanoseconds to seconds
+            g = 1 / (1 + ((w * tau)**2))
+            s = (w * tau) / (1 + ((w * tau)**2))
+            dot, = ax.plot(g, s, marker='o', mfc='none')
+            array = np.linspace(0, g, 50)
+            y = (array * s / g)
+            ax.plot(array, y, color=dot.get_color())

src/napari_flim_phasor_plotter/_widget.py

@@ -120,7 +120,6 @@ def make_flim_phasor_plot(image_layer: "napari.layers.Image",
     # TO DO: avoid using private method access to napari_viewer.window._dock_widgets (will be deprecated)
     dock_widgets_names = [key for key,
                           value in napari_viewer.window._dock_widgets.items()]
-    print(dock_widgets_names)
     if 'Phasor Plotter Widget (napari-flim-phasor-plotter)' not in dock_widgets_names:
         plotter_widget = PhasorPlotterWidget(napari_viewer)
         napari_viewer.window.add_dock_widget(
@@ -145,17 +144,7 @@ def make_flim_phasor_plot(image_layer: "napari.layers.Image",
     plotter_widget.run(labels_layer.features,
                        plotter_widget.plot_x_axis.currentText(),
                        plotter_widget.plot_y_axis.currentText())
-
-    # Redefine axes limits
-    plotter_widget.graphics_widget.axes.autoscale()
-    current_ylim = plotter_widget.graphics_widget.axes.get_ylim()
-    current_xlim = plotter_widget.graphics_widget.axes.get_xlim()
-    ylim_0 = np.amin([current_ylim[0] - 0.1 * current_ylim[0], -0.1])
-    ylim_1 = np.amax([current_ylim[1] + 0.1 * current_ylim[1], 0.7])
-    xlim_0 = np.amin([current_xlim[0] - 0.1 * current_xlim[0], -0.1])
-    xlim_1 = np.amax([current_xlim[1] + 0.1 * current_xlim[1], 1.1])
-    plotter_widget.graphics_widget.axes.set_ylim([ylim_0, ylim_1])
-    plotter_widget.graphics_widget.axes.set_xlim([xlim_0, xlim_1])
+    plotter_widget.redefine_axes_limits(ensure_full_semi_circle_displayed=True)
 
     # Update laser frequency spinbox
     # TO DO: access and update widget in a better way