added three optionals to gui

mtor/__init__.py

@@ -15,13 +15,14 @@ __version__ = "0.1.0"
 
 
 def run():
-    # pw = prescan_workflow("mtor-bilder", 50, 910, 300, 660)
-    pw = prescan_workflow("mtor-bilder", 50, 725 + 150, 300, 725)
+    #pw = prescan_workflow("mtor-bilder", 50, 725 + 150, 300, 725)
+    pw = prescan_workflow("mtor-bilder-2", 125, 795, 275, 700)
     iw = image_workflow(pw.parameters)
     dw = data_workflow(iw.data, iw.parameters)
     fw = postprocessing_workflow(dw.data, dw.parameters)  # noqa: F841
 
 
 def run_data():
+    dw = cached_data_workflow("mtor-bilder-2")  # noqa: F841
     dw = cached_data_workflow("mtor-bilder")  # noqa: F841
     # postprocessing_workflow(dw.data, dw.parameters)  # noqa: F841

mtor/commons.py

@@ -15,8 +15,6 @@ LABEL_DISCARDED = "discarded"
 OUTPUT_FOLDER_NAMES = (
     "colored",
     "cuts",
-    f"cuts_{LABEL_DISCARDED}",
-    f"cuts_{LABEL_SELECTED}",
     "data",
 )
 

mtor/gui.py

@@ -61,6 +61,22 @@ class MtorImageAnalysis(QWidget):
         self.roi_bottom_input.setValidator(QIntValidator())
         self.roi_bottom_input.textChanged.connect(self.check_button_state)
 
+        # aditional parameters
+        self.pad_x_label = QLabel("Roi padding on x axis")
+        self.pad_x_input = QLineEdit()
+        self.pad_x_input.setValidator(QIntValidator())
+        self.pad_x_input.textChanged.connect(self.check_button_state)
+
+        self.pad_y_label = QLabel("Roi padding on y axis")
+        self.pad_y_input = QLineEdit()
+        self.pad_y_input.setValidator(QIntValidator())
+        self.pad_y_input.textChanged.connect(self.check_button_state)
+
+        self.cc_boost_label = QLabel("Intensity factor for colored images")
+        self.cc_boost_input = QLineEdit()
+        self.cc_boost_input.setValidator(QIntValidator())
+        self.cc_boost_input.textChanged.connect(self.check_button_state)
+
         # action buttons
         self.btn_run = QPushButton("Run", self)
         self.btn_run.setEnabled(False)
@@ -94,8 +110,22 @@ class MtorImageAnalysis(QWidget):
 
         grid.addWidget(QLabel(), 8, 0, 1, 2)
 
-        grid.addWidget(self.btn_exit, 9, 0)
-        grid.addWidget(self.btn_run, 9, 1)
+        grid.addWidget(self.pad_x_label, 9, 0)
+        grid.addWidget(self.pad_x_input, 9, 1)
+
+        grid.addWidget(self.pad_y_label, 10, 0)
+        grid.addWidget(self.pad_y_input, 10, 1)
+
+        grid.addWidget(self.cc_boost_label, 11, 0)
+        grid.addWidget(self.cc_boost_input, 11, 1)
+
+        grid.addWidget(self.btn_exit, 12, 0)
+        grid.addWidget(self.btn_run, 12, 1)
+
+        # set default values
+        self.pad_x_input.setText("50")
+        self.pad_y_input.setText("25")
+        self.cc_boost_input.setText("5")
 
         self.setLayout(grid)
         # self.resize(350, 300)
@@ -128,35 +158,37 @@ class MtorImageAnalysis(QWidget):
                 self.check_button_state()
 
     def check_button_state(self):
-        values = self.get_values()
-        self.btn_run.setEnabled(all(values))
-
-    def get_values(self):
-        fields = [
-            (self.dir_selected, str),
-            (self.roi_top_input, int),
-            (self.roi_right_input, int),
-            (self.roi_bottom_input, int),
-            (self.roi_left_input, int),
-        ]
-        result = []
-        for field, func in fields:
+        parameters = self.get_parameters()
+        self.btn_run.setEnabled(all(parameters.values()))
+
+    def get_parameters(self):
+        fields = {
+            '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),
+        }
+        parameters = {key: None for key in fields}
+        for key, name_and_func in fields.items():
+            field, func = name_and_func
             raw_data = field.text().strip()
             if raw_data:
                 if func is int:
                     # in qt5, a point as 1000 separator is allowed
                     raw_data = raw_data.replace(".", "")
-                result.append(func(raw_data))
-            else:
-                result.append(None)
-        return tuple(result)
+                parameters[key] = func(raw_data)
+        return parameters
 
     def run_analysis(self):
-        parameters = self.get_values()
-        if all(parameters):
+        parameters = self.get_parameters()
+        if all(parameters.values()):
             self.analysis_parameters = parameters
-        self.hide()
-        QApplication.instance().quit()
+            self.hide()
+            QApplication.instance().quit()
 
 
 def run_gui():
@@ -165,8 +197,7 @@ def run_gui():
     app.exec_()
 
     if mia.analysis_parameters is not None:
-        analysis_parameters = tuple((p for p in mia.analysis_parameters))
-        pw = prescan_workflow(*analysis_parameters)
+        pw = prescan_workflow(**mia.analysis_parameters)
         iw = image_workflow(pw.parameters)
         dw = data_workflow(iw.data, iw.parameters)
         fw = postprocessing_workflow(dw.data, dw.parameters)

mtor/parameters.py

@@ -19,8 +19,7 @@ class Parameters(dict):
     cut_pad_y:              pixels added to top or bottom edge to crop an image
     cut_right:              right edge for croping an image
     cut_top:                left edge for croping an image
-    cuts_discarded_dir:     path to the directory of discarded croped images
-    cuts_selected_dir:      path to the directory of selected croped images
+    cuts_dir:               path to the directory of croped images
     data_dir:               path to the directory for graphs and numeric data
     folder:                 name of the directory that holds the tif images
     guard_filter_polynom:   polynomal scalar for smoothing the guards histogram
@@ -62,7 +61,7 @@ class Parameters(dict):
         self.folder = folder
 
         # defaults
-        self.boost = 10
+        self.boost = 5
         self.cut_pad_x = 50
         self.cut_pad_y = 25
         self.guard_histogram_bins = 100
@@ -73,7 +72,7 @@ class Parameters(dict):
         self.savgol_filter_window = 51
         self.savgol_filter_polynom = 1
         self.peak_min_distance = 5
-        self.peak_threshold = 0.3
+        self.peak_threshold = 0.2
 
         # labels for data items
         self.roi_name = "roi"

test_mtor.py

@@ -5,5 +5,5 @@ tif_dir = "original_tifs"
 #mtor.process_tifs(tif_dir, 50, 910, 300, 660, boost=5)
 
 
-#mtor.run()
-mtor.run_data()
+mtor.run()
+#mtor.run_data()