Batch mode. this refs #33

Author: JeanBilheux

__code/__init__.py

@@ -89,3 +89,35 @@ class SvmbirParameters(RecParameters):
     weight_type = 'weight type'
     verbose = 'verbose'
     temp_disk = 'temp disk'
+
+
+class BatchJsonKeys:
+
+    list_raw_files = 'list_raw_files'
+    list_ob_files = 'list_ob_files'
+    list_dc_files = 'list_dc_files'
+    crop_region = 'crop_region'
+    gamma_filtering_flag = 'gamma_filtering_flag'
+    beam_fluctuation_flag = 'beam_fluctuation_flag'
+    beam_fluctuation_region = 'beam_fluctuation_region'
+    tilt_value = 'tilt_value'
+    remove_negative_values_flag = 'remove_negative_values_flag'
+    bm3d_flag = 'bm3d_flag'
+    tomopy_v0_flag = 'tomopy_v0_flag'
+    ketcham_flag = 'ketcham_flag'
+    range_slices_to_reconstruct = 'range_slices_to_reconstruct'
+    laminography_dict = 'laminography_dict'
+
+    angle = 'angle'
+    list_gpus = 'list_gpus'
+    num_iterations = 'num_iterations'
+    mrf_p = 'mrf_p'
+    mrf_sigma = 'mrf_sigma'
+    stop_threshold = 'stop_threshold'
+    verbose = 'verbose'
+    debug = 'debug'
+    log_file_name = 'log_file_name'
+
+    filt_cutoff = 'filt_cutoff'
+    filt_type = 'filt_type'
+    

__code/batch_handler.py

@@ -1,6 +1,10 @@
+import os
+
 from __code.parent import Parent
-from __code import DataType
+from __code import DataType, BatchJsonKeys
 from __code.laminography_event_handler import LaminographyEventHandler
+from __code.utilities.time import get_current_time_in_special_file_name_format
+from __code.utilities.json import save_json
 
 
 class BatchHandler(Parent):
@@ -12,19 +16,19 @@ def create_config_file(self):
         list_ob_files = self.parent.input_files[DataType.ob]
         list_dc_files = self.parent.input_files[DataType.dc]
 
-        # crop region
-        crop_left, crop_right, crop_top, crop_bottom = list(self.parent.cropping.result)
+        # crop region (left, right, top, bottom)
+        crop_region = list(self.parent.cropping.result)
 
         ## filter #1
         # gamma filtering flag
         gamma_filtering_flag = self.parent.gamma_filtering_ui.value
 
-        # beam fluctuation correction flag and region
+        # beam fluctuation correction flag and region (left, right, top, bottom)
         beam_fluctuation_flag = self.parent.beam_fluctuation_ui.value
-        bf_left, bf_right, bf_top, bf_bottom = list(self.parent.beam_fluctuation_roi.value)
+        beam_fluctuation_region = list(self.parent.beam_fluctuation_roi.result)
 
         # tilt value
-        tilt_value = self.parent.tilt_options_ui.value
+        tilt_value = self.parent.tilt_option_ui.value
 
         ## filter #2
         # remove negative values
@@ -36,16 +40,53 @@ def create_config_file(self):
         ketcham_flag = self.parent.ring_removal_ui.children[2].value
 
         # range of slices to reconstruct
-        top_slice, bottom_slice = list(self.parent.z_range_selection.result)
+        range_slices_to_reconstruct = list(self.parent.z_range_selection.result)
 
         # laminography parameters
-        laminography_dict = self.parent.laminography_settings_ui
-        angle = laminography_dict['angle'].value
-        list_gpu_index = LaminographyEventHandler(laminography_dict['list_gpus'])
-        num_iter = laminography_dict['num_iterations'].value
-        mrf_p = laminography_dict['mrf_p'].value
-        mrf_sigma = laminography_dict['mrf_sigma'].value
-        stop_threhsold = laminography_dict['stop_threshold'].value
-        verbose = laminography_dict['verbose'].value
-
-        json_file_name =  pass
+        ui_laminography_dict = self.parent.laminography_settings_ui
+        angle = ui_laminography_dict[BatchJsonKeys.angle].value
+        list_gpu_index = LaminographyEventHandler.get_gpu_index(laminography_dict[BatchJsonKeys.list_gpus])
+        num_iter = ui_laminography_dict[BatchJsonKeys.num_iterations].value
+        mrf_p = ui_laminography_dict[BatchJsonKeys.mrf_p].value
+        mrf_sigma = ui_laminography_dict[BatchJsonKeys.mrf_sigma].value
+        stop_threhsold = ui_laminography_dict[BatchJsonKeys.stop_threshold].value
+        verbose = ui_laminography_dict[BatchJsonKeys.verbose].value
+        laminograph_dict = {BatchJsonKeys.angle: angle,
+                            BatchJsonKeys.list_gpus: list_gpu_index,
+                            BatchJsonKeys.num_iterations: num_iter,
+                            BatchJsonKeys.mrf_p: mrf_p,
+                            BatchJsonKeys.mrf_sigma: mrf_sigma,
+                            BatchJsonKeys.stop_threshold: stop_threhsold,
+                            BatchJsonKeys.verbose: verbose}
+
+
+        # create json dictionary
+        json_dictionary = {BatchJsonKeys.list_raw_files: list_raw_files,
+                           BatchJsonKeys.list_ob_files: list_ob_files,
+                           BatchJsonKeys.list_dc_files: list_dc_files,
+                           BatchJsonKeys.crop_region: crop_region,
+                           BatchJsonKeys.gamma_filtering_flag: gamma_filtering_flag,
+                           BatchJsonKeys.beam_fluctuation_flag:beam_fluctuation_flag,
+                           BatchJsonKeys.beam_fluctuation_region: beam_fluctuation_region,
+                           BatchJsonKeys.tilt_value: tilt_value,
+                           BatchJsonKeys.remove_negative_values_flag: remove_negative_values_flag,
+                           BatchJsonKeys.bm3d_flag: bm3d_flag,
+                           BatchJsonKeys.tomopy_v0_flag: tomopy_v0_flag,
+                           BatchJsonKeys.ketcham_flag: ketcham_flag,
+                           BatchJsonKeys.range_slices_to_reconstruct: range_slices_to_reconstruct,
+                           BatchJsonKeys.laminography_dict: laminography_dict,
+                           }
+
+        _current_time = get_current_time_in_special_file_name_format()
+        base_folder_name = self.parent.raw_folder_name
+        json_file_name = os.path.join(os.path.expanduser("~"), 
+                                      f"laminography_{base_folder_name}_{_current_time}.json")
+
+        log_file_name = os.path.join(os.path.expanduser("~"),
+                                     f"laminography_{base_folder_name}_{_current_time}.cfg")
+
+        # print(f"{json_dictionary =}")
+
+        save_json(json_file_name=json_file_name,
+                  json_dictionary=json_dictionary)
+        

__code/laminography_event_handler.py

@@ -12,6 +12,7 @@
 from __code.system import System
 from __code.utilities.files import save_json
 from __code.utilities.time import convert_time_s_in_time_hr_mn_s
+from __code import BatchJsonKeys
 
 
 class LaminographyEventHandler:
@@ -88,13 +89,13 @@ def set_settings(self):
         display(tab)
 
         # saving widgets for batch mode
-        self.parent.laminography_settings_ui = {'angle': self.laminography_angle_ui,
-                                                'list_gpus': self.children_gpus,
-                                                'num_iterations': self.num_iter_ui,
-                                                'mrf_p': self.mrf_p_ui,
-                                                'mrf_sigma': self.mrf_sigma_ui,
-                                                'stop_threshold': self.stop_threshold_ui,
-                                                'verbose': self.verbose_ui}
+        self.parent.laminography_settings_ui = {BatchJsonKeys.angle: self.laminography_angle_ui,
+                                                BatchJsonKeys.list_gpus: self.children_gpus,
+                                                BatchJsonKeys.num_iterations: self.num_iter_ui,
+                                                BatchJsonKeys.mrf_p: self.mrf_p_ui,
+                                                BatchJsonKeys.mrf_sigma: self.mrf_sigma_ui,
+                                                BatchJsonKeys.stop_threshold: self.stop_threshold_ui,
+                                                BatchJsonKeys.verbose: self.verbose_ui}
 
     @staticmethod
     def get_gpu_index(children_gpus_ui):
@@ -106,19 +107,19 @@ def get_gpu_index(children_gpus_ui):
 
     def get_rec_params(self):
         rec_params = {}
-        rec_params['num_iter'] = self.num_iter_ui.value
-        rec_params['gpu_index'] = LaminographyEventHandler.get_gpu_index(self.children_gpus[1:])
-        rec_params['MRF_P'] = self.mrf_p_ui.value
-        rec_params['MRF_SIGMA'] = self.mrf_sigma_ui.value
+        rec_params[BatchJsonKeys.num_iterations] = self.num_iter_ui.value
+        rec_params[BatchJsonKeys.list_gpus] = LaminographyEventHandler.get_gpu_index(self.children_gpus[1:])
+        rec_params[BatchJsonKeys.mrf_p] = self.mrf_p_ui.value
+        rec_params[BatchJsonKeys.mrf_sigma] = self.mrf_sigma_ui.value
         # rec_params['huber_T'] = self.huber_t
         # rec_params['huber_delta'] = self.huber_delta
         # rec_params['sigma'] = self.sigma
         # rec_params['reject_frac'] = self.reject_frac
-        rec_params['verbose'] = self.verbose_ui.value
-        rec_params['debug'] = self.debug
-        rec_params['stop_thresh'] = self.stop_threshold_ui.value
-        rec_params['filt_cutoff'] = 0.5
-        rec_params['filt_type'] = 'Ram-Lak'
+        rec_params[BatchJsonKeys.verbose] = self.verbose_ui.value
+        rec_params[BatchJsonKeys.debug] = self.debug
+        rec_params[BatchJsonKeys.stop_threshold] = self.stop_threshold_ui.value
+        rec_params[BatchJsonKeys.filt_cutoff] = 0.5
+        rec_params[BatchJsonKeys.filt_type] = 'Ram-Lak'
 
         return rec_params
 

__code/laminographyui.py

@@ -97,6 +97,9 @@ class LaminographyUi:
     ob_raw = None
     dc_raw = None
 
+    # name of the raw folder
+    raw_folder_name = None
+
     investigate_data_flag = False
 
     o_tilt = None
@@ -116,6 +119,7 @@ def __init__(self, working_dir="./"):
         self.working_dir[DataType.raw] = os.path.join(init_path_to_raw, default_input_folder[DataType.raw])
         self.working_dir[DataType.ob] = os.path.join(init_path_to_raw, default_input_folder[DataType.ob])
         self.working_dir[DataType.dc] = os.path.join(init_path_to_raw, default_input_folder[DataType.dc])
+        print("version 07-30-2024")
 
     # SELECT INPUT DATA ===============================================================================================
     def select_raw(self):

__code/laminographyui_batch_mode.py

@@ -105,6 +105,9 @@ class LaminographyUi:
     ob_raw = None
     dc_raw = None
 
+    # name of the raw folder
+    raw_folder_name = None
+
     investigate_data_flag = False
 
     o_tilt = None
@@ -168,6 +171,7 @@ def define_parameters(self):
         self.display_section_title(name='Beam fluctuation')
         o_beam = BeamFluctuationCorrection(parent=self)
         o_beam.beam_fluctuation_correction_option()
+        o_beam.apply_select_beam_fluctuation(batch_mode=True)
 
         self.display_section_title(name='Tilt calculation')
         self.tilt_correction_options()

__code/utilities/json.py

@@ -0,0 +1,17 @@
+import json
+import os
+
+
+def load_json(json_file_name):
+    if not os.path.exists(json_file_name):
+        return None
+
+    with open(json_file_name) as json_file:
+        data = json.load(json_file)
+
+    return data
+
+
+def save_json(json_file_name, json_dictionary=None):
+    with open(json_file_name, 'w') as outfile:
+        json.dump(json_dictionary, outfile)

__code/workflow/load.py

@@ -76,13 +76,6 @@ def load_percentage_of_data(self, percentage_to_load=5):
                       max_workers=20)  # use 20 workers
         )
 
-
-
-
-
-
-
-
     def load_data(self):
 
         self.parent.proj_raw, self.parent.ob_raw, self.parent.dc_raw, self.parent.rot_angles = (
@@ -100,6 +93,12 @@ def load_data(self):
 
             self.parent.dc_raw = np.array([np.zeros_like(self.parent.proj_raw[0])])
 
+        # debugging - use np.float16 instead of default np.float64
+        print(f"Before conversion: {self.parent.proj_raw.dtype= }")
+        # self.parent.proj_raw = self.parent.proj_raw.astype(np.float16)
+        # self.parent.ob_raw = self.parent.ob_raw.astype(np.float16)
+        # self.parent.dc_raw = self.parent.dc_raw.astype(np.float16)
+        # print(f"After conversion: {self.parent.proj_raw.dtype= }")
         self.parent.untouched_sample_data = copy.deepcopy(self.parent.proj_raw)
 
     def select_dc_options(self):

__code/workflow/tilt.py

@@ -533,13 +533,15 @@ def plot_comparisons(algo_selected, color_range, col, row, zoom_x, zoom_y):
         display(self.test_tilt)
 
     def display_batch_options(self):
-        self.parent.tilt_options_ui = widgets.VBox([
+        tilt_options_ui = widgets.VBox([
             widgets.Label("Tilt value (degrees)",
                           layout=widgets.Layout(width='200px'),
                           ),
             widgets.FloatSlider(min=-90,
                                 max=90,
                                 value=0)
         ])
-        display(self.parent.tilt_options_ui)
+        display(tilt_options_ui)
+
+        self.parent.tilt_option_ui = tilt_options_ui.children[1]