updated installation to include scikit-image, made minor changes to u…

…nwrap functionality

cohere-defaults/config_disp

@@ -10,5 +10,9 @@ crop = [.5, .5, .5]
                            // fractions of the image array dimensions assigned to cropped array dimensions
                            // default [1.0, 1.0, 1.0] meaning the whole array
 
+unwrap = False
+                           // if True the vts file will contain unwrapped phase in addition to
+                           // phase and amplitude
+
 make_twin = False
                            // switch to whether visualize twin image

cohere-scripts/beamline_visualization.py

@@ -65,7 +65,7 @@ def __init__(self, crop, geometry):
         self.recipspace_uptodate = 0
 
 
-    def visualize(self, image, support, coh, save_dir, is_twin=False):
+    def visualize(self, image, support, coh, save_dir, unwrap=False, is_twin=False):
         """
         Manages visualization process. Saves the results in a given directory in files: image.vts, support.vts, and coherence.vts. If is_twin then the saved files have twin prefix.
         Parameters
@@ -83,6 +83,12 @@ def visualize(self, image, support, coh, save_dir, is_twin=False):
         """
         save_dir = save_dir.replace(os.sep, '/')
         arrays = {"imAmp": abs(image), "imPh": np.angle(image)}
+
+          # unwrap phase here
+        if unwrap:
+            from skimage import restoration
+            arrays['imUwPh'] = restoration.unwrap_phase(arrays['imPh'])
+
         self.add_ds_arrays(arrays)
         if is_twin:
             self.write_directspace(save_dir + '/twin_image')
@@ -252,7 +258,7 @@ def write_recipspace(self, filename, **args):
         print('saved file', filename)
 
 
-def process_dir(instrument, config_map, rampups, crop, make_twin, res_dir_scan):
+def process_dir(instrument, config_map, rampups, crop, unwrap, make_twin, res_dir_scan):
     """
     Loads arrays from files in results directory. If reciprocal array exists, it will save reciprocal info in tif format. It calls the save_CX function with the relevant parameters.
     Parameters
@@ -309,7 +315,7 @@ def process_dir(instrument, config_map, rampups, crop, make_twin, res_dir_scan):
 
     crop = crop + [1.0] * (len(image.shape) - len(crop))
     viz = CXDViz(crop, geometry)
-    viz.visualize(image, support, coh, save_dir)
+    viz.visualize(image, support, coh, save_dir, unwrap)
 
     if make_twin:
         image = np.conjugate(np.flip(image))
@@ -318,7 +324,7 @@ def process_dir(instrument, config_map, rampups, crop, make_twin, res_dir_scan):
             image, support = ut.center(image, support)
         if rampups > 1:
             image = ut.remove_ramp(image, ups=rampups)
-        viz.visualize(image, support, coh, save_dir, True)
+        viz.visualize(image, support, coh, save_dir, unwrap, True)
 
 
 def handle_visualization(experiment_dir, rec_id=None):
@@ -412,6 +418,11 @@ def handle_visualization(experiment_dir, rec_id=None):
         else:
             crop = []
 
+        if 'unwrap' in disp_config_map:
+            unwrap = disp_config_map['unwrap']
+        else:
+            unwrap = False
+
         if 'results_dir' in disp_config_map:
             results_dir = disp_config_map['results_dir'].replace(os.sep, '/')
         elif separate:
@@ -447,9 +458,9 @@ def handle_visualization(experiment_dir, rec_id=None):
             dirs = [[dir, last_scan] for dir in dirs]
 
         if len(dirs) == 1:
-            process_dir(instrument, config_map, rampups, crop, make_twin, dirs[0])
+            process_dir(instrument, config_map, rampups, crop, unwrap, make_twin, dirs[0])
         else:
-            func = partial(process_dir, instrument, config_map, rampups, crop, make_twin)
+            func = partial(process_dir, instrument, config_map, rampups, crop, unwrap, make_twin)
             no_proc = min(cpu_count(), len(dirs))
             with Pool(processes = no_proc) as pool:
                pool.map_async(func, dirs)

cohere-scripts/beamlines/aps_34idc/beam_tabs.py

@@ -381,6 +381,9 @@ def init(self, tabs, main_window):
         self.make_twin = QCheckBox('make twin')
         self.make_twin.setChecked(False)
         layout.addWidget(self.make_twin)
+        self.unwrap = QCheckBox('include unwrapped phase')
+        self.unwrap.setChecked(False)
+        layout.addWidget(self.unwrap)
         self.crop = QLineEdit()
         layout.addRow("crop", self.crop)
         self.rampups = QLineEdit()
@@ -414,7 +417,6 @@ def load_tab(self, conf_map):
         # Do not update results dir, as it may point to a wrong experiment if
         # it's loaded from another
 
-         # if parameters are configured, override the readings from spec file
         if 'make_twin' in conf_map:
             make_twin = conf_map['make_twin']
             if make_twin:
@@ -424,6 +426,15 @@ def load_tab(self, conf_map):
         else:
             self.make_twin.setChecked(False)
 
+        if 'unwrap' in conf_map:
+            unwrap = conf_map['unwrap']
+            if unwrap:
+                self.unwrap.setChecked(True)
+            else:
+                self.unwrap.setChecked(False)
+        else:
+            self.unwrap.setChecked(False)
+
         if 'crop' in conf_map:
             self.crop.setText(str(conf_map['crop']).replace(" ", ""))
         if 'rampups' in conf_map:
@@ -433,6 +444,7 @@ def load_tab(self, conf_map):
     def clear_conf(self):
         self.result_dir_button.setText('')
         self.make_twin.setChecked(False)
+        self.unwrap.setChecked(False)
         self.crop.setText('')
         self.rampups.setText('')
 
@@ -472,6 +484,8 @@ def get_disp_config(self):
             conf_map['results_dir'] = str(self.result_dir_button.text()).replace(os.sep, '/')
         if self.make_twin.isChecked():
             conf_map['make_twin'] = True
+        if self.unwrap.isChecked():
+            conf_map['unwrap'] = True
         if len(self.crop.text()) > 0:
             conf_map['crop'] = ast.literal_eval(str(self.crop.text()).replace('\n', ''))
         if len(self.rampups.text()) > 0:

install_pkgs.bat

@@ -4,3 +4,4 @@ pip install xrayutilities
 pip install psutil
 pip install gputil
 conda install pyqt
+python -m pip install -U scikit-image

install_pkgs.sh

@@ -3,3 +3,4 @@ conda install xrayutilities -c conda-forge
 conda install psutil -c conda-forge
 conda install gputil -c conda-forge
 conda install pyqt -c conda-forge
+python -m pip install -U scikit-image