linted the project

mtor/commons.py

@@ -12,11 +12,7 @@ IMG_MAX_INTENSITY = 65535  # 2^16 -  1
 LABEL_SELECTED = "selected"
 LABEL_DISCARDED = "discarded"
 
-OUTPUT_FOLDER_NAMES = (
-    "colored",
-    "cuts",
-    "data",
-)
+OUTPUT_FOLDER_NAMES = ("colored", "cuts", "data")
 
 RE_DIGITS = re.compile(r"(\d+)")
 

mtor/dataproc.py

@@ -116,7 +116,9 @@ def find_guard_threshold(data_frame, parameters):
     guard_data = numpy.histogram(
         guard_values, bins=parameters.guard_histogram_bins
     )
-    guard_counts = numpy.concatenate([[0], guard_data[0]]).astype(numpy.float16)
+    guard_counts = numpy.concatenate([[0], guard_data[0]]).astype(
+        numpy.float16
+    )
     guard_edges = guard_data[1]  # edges enclose the counts
 
     pyplot.clf()
@@ -410,8 +412,9 @@ def create_report(data_frame, selected_df, extremas_df, parameters):
         text_and_graph(
             4,
             (
-                "The images with one of the guard values above the threshold "
-                "are discarded."
+                f"{num_discarded} images with one of the guard values above "
+                f"the threshold are discarded, leaving {num_selected} "
+                f"selected images."
             ),
         ),
         Image(

mtor/gui.py

@@ -27,6 +27,7 @@ from .workflows import (
 
 PARAMETERS_FILE = "mia-gui-parameters.json"
 
+
 class MtorImageAnalysis(QWidget):
     def __init__(self):
         super().__init__()
@@ -89,14 +90,14 @@ class MtorImageAnalysis(QWidget):
         self.btn_exit.clicked.connect(QApplication.instance().quit)
 
         self.fields_map = {
-            'folder': (self.dir_selected, str),
-            'top': (self.roi_top_input, int),
-            'right': (self.roi_right_input, int),
-            'bottom': (self.roi_bottom_input, int),
-            'left': (self.roi_left_input, int),
-            'cut_pad_x': (self.pad_x_input, int),
-            'cut_pad_y': (self.pad_y_input, int),
-            'boost': (self.cc_boost_input, int),
+            "folder": (self.dir_selected, str),
+            "top": (self.roi_top_input, int),
+            "right": (self.roi_right_input, int),
+            "bottom": (self.roi_bottom_input, int),
+            "left": (self.roi_left_input, int),
+            "cut_pad_x": (self.pad_x_input, int),
+            "cut_pad_y": (self.pad_y_input, int),
+            "boost": (self.cc_boost_input, int),
         }
 
         # Layout
@@ -203,7 +204,9 @@ class MtorImageAnalysis(QWidget):
             parameter_path = Path(parameters["folder"]) / PARAMETERS_FILE
             try:
                 with parameter_path.open("w") as fh:
-                    tmp = {k: v for k, v in parameters.items() if k != "folder"}
+                    tmp = {
+                        k: v for k, v in parameters.items() if k != "folder"
+                    }
                     print(tmp)
                     json.dump(tmp, fh)
             except Exception:

mtor/postproc.py

@@ -67,4 +67,3 @@ def rename_cut_images(file_stems, parameters):
             )
             new_path = path.with_name(f"{path.stem}_cut_{label}{path.suffix}")
             path.rename(new_path)
-

mtor/workflows.py

@@ -53,12 +53,13 @@ def image_workflow(parameters):
 
 
 def data_workflow(stats_results, parameters):
-    from .dataproc import save_temp
-
     print("3/5: Data analysis")
     set_plotting_styles()
     data_frame = construct_data_frame(stats_results, parameters)
-    # save_temp(data_frame, parameters)  # enable this for the main run_test_data
+
+    # uncomment the next two lines to use the main run_test_data
+    # from .dataproc import save_temp
+    # save_temp(data_frame, parameters)
 
     find_guard_threshold(data_frame, parameters)
     data_frame = check_guards(data_frame, parameters)