fix gui

README.md

@@ -45,7 +45,7 @@ For running tests:
 pip install .[test]
 ```
 
-For using the GUI:
+For using the GUI (experimentally at this stage!!! see [gui doc section](#gui)):
 ```cmd
 pip install .[gui]
 ```
@@ -123,6 +123,12 @@ with synpivimage.HDF5Writer(case_name="test_case",
     hw.writeB(0, imgB, partB)
 ```
 
+## GUI
+Is experimental and more for demonstrating and debugging purposes.
+
+
+Go to `synpivimage/gui` and run `python core.py` to start the GUI.
+
 ## Developers
 
 ### Testing

setup.cfg

@@ -44,7 +44,9 @@ test =
     pylint
 gui =
     PyQt5
+    xarray
 complete =
+    %(gui)s
     %(test)s
 
 

synpivimage/gui/core.py

@@ -265,6 +265,7 @@ def generate_images(self, take_existing_particles=False):
             else:
                 particle_dataA = synpivimage.particles.Particles.generate(
                     dx_max=dx_max, dy_max=dy_max, dz_max=dz_max,
+                    size=2.,  # TODO: should not be default
                     camera=cam,
                     laser=laser,
                     ppp=self.particle_density.value(),
@@ -468,13 +469,15 @@ def _plot_correlation(self):
             self.axes[3][0].plot(z, laser_intensity)
             # self.axes[4][0].plot(z, laser_intensity)
 
-            self.axes[3][1].scatter(self.particle_dataA[self.curr_img_index].z, self.particle_dataA[self.curr_img_index].y,
+            self.axes[3][1].scatter(self.particle_dataA[self.curr_img_index].z,
+                                    self.particle_dataA[self.curr_img_index].y,
                                     color='b', alpha=0.5, s=10, marker='o')
             # draw vlines for laser
             self.axes[3][1].vlines(-self.laser_width.value() / 2, 0, self.nx.value(), color='k', linestyle='--')
             self.axes[3][1].vlines(self.laser_width.value() / 2, 0, self.nx.value(), color='k', linestyle='--')
 
-            self.axes[3][1].scatter(self.particle_dataB[self.curr_img_index].z, self.particle_dataB[self.curr_img_index].y,
+            self.axes[3][1].scatter(self.particle_dataB[self.curr_img_index].z,
+                                    self.particle_dataB[self.curr_img_index].y,
                                     color='r', alpha=0.5, s=10, marker='o')
             self.axes[3][1].vlines(-self.laser_width.value() / 2, 0, self.nx.value(), color='k', linestyle='--')
             self.axes[3][1].vlines(self.laser_width.value() / 2, 0, self.nx.value(), color='k', linestyle='--')