new cases in place. this refs #241

Author: JeanBilheux

notebooks/__code/normalization_tof/normalization_for_timepix.py

@@ -77,7 +77,7 @@ def load_data_using_multithreading(list_tif: list = None, combine_tof: bool = Fa
     if combine_tof:
         return np.array(data).sum(axis=0)
     else:
-        return np.array(data)
+        return np.array(data, dtype=np.float32)
 
 
 def retrieve_list_of_tif(folder: str) -> list:
@@ -223,7 +223,7 @@ def normalization_with_list_of_runs(sample_run_numbers: list = None,
         if verbose:
             display(HTML(f"Normalization of run {_sample_run_number}"))
 
-        _sample_data = np.array(sample_master_dict[_sample_run_number][MasterDictKeys.data], dtype=np.float32)
+        _sample_data = sample_master_dict[_sample_run_number][MasterDictKeys.data]
 
         # get statistics of sample data
         data_shape = _sample_data.shape
@@ -269,11 +269,13 @@ def normalization_with_list_of_runs(sample_run_numbers: list = None,
         # _sample_data = np.divide(_sample_data, ob_data_combined, out=np.zeros_like(_sample_data), where=ob_data_combined!=0)
         # _sample_data = np.divide(_sample_data, ob_data_combined, out=np.zeros_like(_sample_data))
         # _sample_data = np.divide(_sample_data, ob_data_combined, out=np.zeros_like(_sample_data), where=ob_data_combined!=0)
-        _normalized_data = np.zeros_like(_sample_data, dtype=np.float32)
-        index = 0
-        for _sample, _ob in zip(_sample_data, ob_data_combined):
-            _normalized_data[index] = np.divide(_sample, _ob)
-            index += 1
+        # _normalized_data = np.zeros_like(_sample_data, dtype=np.float32)
+        # index = 0
+        _normalized_data = np.divide(_sample_data, ob_data_combined)
+
+        # for _sample, _ob in zip(_sample_data, ob_data_combined):
+        #     _normalized_data[index] = np.divide(_sample, _ob)
+        #     index += 1
 
         normalized_data[_sample_run_number] = _normalized_data
 
@@ -479,7 +481,7 @@ def normalization(sample_folder=None, ob_folder=None, output_folder="./", verbos
 
 
 def make_tiff(data: list, filename: str = "", metadata: dict = None) -> None:
-    new_image = Image.fromarray(np.array(data))
+    new_image = Image.fromarray(np.array(data), mode='F')
     if metadata:
         new_image.save(filename, tiffinfo=metadata)
     else:
@@ -754,8 +756,8 @@ def combine_ob_images(ob_master_dict: dict,
             logging.info(f"{temp_ob_data.shape = }")
             ob_data = temp_ob_data.copy()
 
-        ob_data_combined = np.array(ob_data).mean(axis=0)
-        logging.info(f"{ob_data_combined.shape = }")
+        # ob_data_combined = np.array(ob_data).mean(axis=0)
+        # logging.info(f"{ob_data_combined.shape = }")
 
         # remove zeros
         if replace_ob_zeros_by_nan:
@@ -778,8 +780,10 @@ def combine_ob_images(ob_master_dict: dict,
         full_ob_data_corrected.append(ob_data)
         logging.info(f"{np.shape(full_ob_data_corrected) = }")
 
+    logging.info(f"Combining all ob images is done!")
+    logging.info(f"\tbefore: {len(full_ob_data_corrected) = }")
     ob_data_combined = np.array(full_ob_data_corrected).mean(axis=0)
-    logging.info(f"{ob_data_combined.shape = }")
+    logging.info(f"\tafter: {ob_data_combined.shape = }")
 
     # remove zeros
     if replace_ob_zeros_by_nan:

notebooks/__code/rename_files/rename_files.py

@@ -63,7 +63,7 @@ def define_new_naming_schema(self):
             self.o_schema.show()
 
 
-class NamingSchemaDefinition(object):
+class NamingSchemaDefinition:
     ext = ''
     list_files = []
     working_dir = ''
@@ -100,12 +100,16 @@ def new_naming_schema(self):
         else:
             prefix = self.basename_selected_by_user.value
 
-        post_index_separator = self.box5.children[1].value
         nbr_digits = self.box7.children[1].value
+        if self.suffix_box2.children[1].value:
+            suffix = self.suffix_box2.children[2].value
+        else:
+            suffix = nbr_digits * '#'
 
         ext = self.box9.children[1].value
 
-        schema = prefix + post_index_separator + nbr_digits * '#' + ext
+        post_index_separator = self.box5.children[1].value
+        schema = prefix + post_index_separator + suffix + ext
         return schema
 
     def pre_index_text_changed(self, sender):
@@ -130,6 +134,20 @@ def changed_use_new_prefix_name(self, value=[]):
         self.new_prefix_text_widget.disabled = not _value
         self.post_text_changed(None)
 
+    def changed_use_digit_suffix_name(self, value=[]):
+        self.user_new_suffix_widget.value = not value['new']
+        self.new_suffix_text_widget.disabled = value['new']
+        self.post_text_changed(None)
+
+    def changed_use_new_suffix_name(self, value=[]):
+        if value == []:
+            _value = self.user_new_suffix_widget.value
+        else:
+            _value = value['new']
+        self.use_digit_suffix_widget.value = not _value
+        self.new_suffix_text_widget.disabled = not _value
+        self.post_text_changed(None)
+
     def get_basename_of_current_dropdown_selected_file(self, is_with_ext=False):
         full_file_name = self.random_input_checkbox.value
         if is_with_ext:
@@ -193,15 +211,15 @@ def show(self):
         # new naming schema
         box_text_width = '10%'
         self.box1 = widgets.HBox([widgets.Label("New prefix File Name",
-                                                layout=widgets.Layout(width='10%')),
+                                                layout=widgets.Layout(width='20%')),
                                   widgets.Checkbox(value=True,
                                                    description='Use previous prefix name',
                                                    layout=widgets.Layout(width='30%'))])
         self.use_previous_prefix_widget = self.box1.children[1]
         self.box1.children[1].observe(self.changed_use_previous_prefix_name, names='value')
 
         self.box1b = widgets.HBox([widgets.Label("",
-                                                 layout=widgets.Layout(width='10%')),
+                                                 layout=widgets.Layout(width='20%')),
                                    widgets.Checkbox(value=False,
                                                     description='Use new prefix',
                                                     layout=widgets.Layout(width='20%')),
@@ -213,6 +231,30 @@ def show(self):
         self.user_new_prefix_widget = self.box1b.children[1]
         self.user_new_prefix_widget.observe(self.changed_use_new_prefix_name, names='value')
 
+
+
+
+        self.suffix_box1 = widgets.HBox([widgets.Label("New suffix File Name",
+                                                layout=widgets.Layout(width='20%')),
+                                  widgets.Checkbox(value=True,
+                                                   description='Use digit suffix',
+                                                   layout=widgets.Layout(width='30%'))])
+        self.use_digit_suffix_widget = self.suffix_box1.children[1]
+        self.suffix_box1.children[1].observe(self.changed_use_digit_suffix_name, names='value')
+
+        self.suffix_box2 = widgets.HBox([widgets.Label("",
+                                                 layout=widgets.Layout(width='20%')),
+                                   widgets.Checkbox(value=False,
+                                                    description='Use new suffix',
+                                                    layout=widgets.Layout(width='20%')),
+                                   widgets.Text(value='',
+                                                disabled=True,
+                                                layout=widgets.Layout(width='25%'))])
+        self.suffix_box2.children[2].observe(self.changed_use_new_suffix_name, names='value')
+        self.user_new_suffix_widget = self.suffix_box2.children[1]
+        self.new_suffix_text_widget = self.suffix_box2.children[2]
+        self.user_new_suffix_widget.observe(self.changed_use_new_suffix_name, names='value')
+
         self.box5 = widgets.HBox([widgets.Label("New Index Separator",
                                                 layout=widgets.Layout(width='15%')),
                                   widgets.Text(value='_',
@@ -245,7 +287,8 @@ def show(self):
         self.box8.children[1].on_trait_change(self.post_text_changed, 'value')
         self.box9.children[1].on_trait_change(self.post_text_changed, 'value')
 
-        after = widgets.VBox([self.box1, self.box1b, self.box5, self.box7, self.box8, self.box9, self.box6])
+        after = widgets.VBox([self.box1, self.box1b, self.suffix_box1, self.suffix_box2, 
+                              self.box5, self.box7, self.box8, self.box9, self.box6])
 
         accordion = widgets.Accordion(children=[before, after])
         accordion.set_title(0, 'Current Schema Name')
@@ -276,6 +319,12 @@ def demo_output_file_name(self):
         input_file = self.get_basename_of_current_dropdown_selected_file(is_with_ext=False)
         self.output_ui_2.children[1].value = input_file
 
+
+        new_name = self.box6.children[1].value
+        self.output_ui_3.children[1].value = new_name
+
+        return
+
         old_index_separator = self.get_old_index_separator()
         new_prefix_name = self.get_new_prefix_name()
         new_index_separator = self.get_new_index_separator()
@@ -284,6 +333,11 @@ def demo_output_file_name(self):
         ext = self.box9.children[1].value
         [start_index, end_index] = self.int_range_slider.value
 
+        print(f"{old_index_separator=}, {new_prefix_name=}")
+        print(f"{new_index_separator=}, {new_number_of_digits=}, {offset=}, {ext=}")
+        print(f"{start_index=}, {end_index=}")
+
+
         try:
             display(HTML("""
 						  <style>
@@ -342,32 +396,47 @@ def get_new_number_of_digits(self):
         return self.box7.children[1].value
 
     def generate_new_file_name(self, old_file_name,
+                               file_index,
                                start_index,
                                end_index,
                                old_index_separator,
                                new_prefix_name,
                                new_index_separator,
                                new_number_of_digits,
                                offset,
+                               suffix_flag, 
+                               suffix,
                                ext):
 
+        file_index += offset
+
         [_pre_extension, _] = os.path.splitext(old_file_name)
-        _name_separated = _pre_extension.split(old_index_separator)
+        # _name_separated = _pre_extension.split(old_index_separator)
+        # print(f"Name separated: {_name_separated}")
 
         if self.user_new_prefix_widget.value == True:
             prefix = new_prefix_name
         else:
             prefix = old_file_name[start_index: end_index + 1]
 
-        try:
-            _index = int(_name_separated[-1]) + offset
+        # try:
+            # print(f"Trying to parse index from {_name_separated[-1]}")
+            # _index = int(_name_separated[-1]) + offset
+            # print(f"Parsed index: {_index}")
+        if suffix_flag:
             new_name = prefix + new_index_separator + \
-                       '{:0{}}'.format(_index, new_number_of_digits) + \
-                       ext
-        except ValueError:
-            _index = _name_separated[-1]
+                        '{:0{}}'.format(file_index, new_number_of_digits) + \
+                    new_index_separator + suffix + ext
+        else:
             new_name = prefix + new_index_separator + \
-                _index + ext
+                        '{:0{}}'.format(file_index, new_number_of_digits) + ext
+        
+        # except ValueError:
+        #     # print(f"Could not parse index from {_name_separated[-1]}")
+        #     # _index = _name_separated[-1]
+        #     new_name = prefix + new_index_separator + \
+        #         _index + ext
+        #     print(f"New name without index: {new_name}")
 
         return new_name
 
@@ -386,19 +455,30 @@ def get_dict_old_new_filenames(self):
         offset = self.box8.children[1].value
         ext = self.box9.children[1].value
 
+        suffix_flag = self.suffix_box2.children[1].value
+        if suffix_flag:
+            suffix = self.suffix_box2.children[2].value
+        else:
+            suffix = ""
+
         list_of_input_basename_files = [os.path.basename(_file) for _file in list_of_input_files]
 
         new_list = {}
         for _file_index, _file in enumerate(list_of_input_basename_files):
+
             new_name = self.generate_new_file_name(_file,
+                                                   _file_index,
                                                    start_index,
                                                    end_index,
                                                    old_index_separator,
                                                    new_prefix_name,
                                                    new_index_separator,
                                                    new_number_of_digits,
                                                    offset,
+                                                   suffix_flag, 
+                                                   suffix,
                                                    ext)
+            
             new_list[list_of_input_files[_file_index]] = new_name
             renaming_result.append("{} \t --> \t {}".format(_file, new_name))
 

notebooks/rename_files.ipynb

@@ -152,7 +152,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "python310",
    "language": "python",
    "name": "python3"
   },