diff --git a/src/toffy/watcher_callbacks.py b/src/toffy/watcher_callbacks.py index 895dccbf..be4f4214 100644 --- a/src/toffy/watcher_callbacks.py +++ b/src/toffy/watcher_callbacks.py @@ -158,22 +158,20 @@ def _generate_fov_data( **kwargs (dict): Unused kwargs for other functions """ - # NOTE: most panels will be specified from (-0.3, 0), modify to (-0.3, -0.06) for deficient - panel_def = modify_panel_ranges(panel, start_offset=0, stop_offset=-0.06) self.__fov_data = extract_bin_files( data_dir=self.run_folder, out_dir=None, include_fovs=[self.point_name], - panel=panel_def, + panel=panel, intensities=intensities, replace=replace, time_res=time_res, ) - self.__panel = panel_def + self.__panel = panel if extract_prof: - # modify from (-0.3, 0) to (-0.06, 0.3) for proficient - panel_prof = modify_panel_ranges(panel, start_offset=0.24, stop_offset=0.3) + # modify from (-0.3, 0) to (0, 0.3) for proficient + panel_prof = modify_panel_ranges(panel, start_offset=0.3, stop_offset=0.3) self.__fov_data_prof = extract_bin_files( data_dir=self.run_folder, out_dir=None, diff --git a/templates/3b_extract_images_from_bin.ipynb b/templates/3b_extract_images_from_bin.ipynb index 45f042ae..f3cae308 100644 --- a/templates/3b_extract_images_from_bin.ipynb +++ b/templates/3b_extract_images_from_bin.ipynb @@ -105,12 +105,12 @@ "metadata": {}, "outputs": [], "source": [ - "# base extraction\n", - "extract_missing_fovs(base_dir, extraction_dir, modify_panel_ranges(panel, stop_offset=-0.06))\n", + "# base deficient extraction\n", + "extract_missing_fovs(base_dir, extraction_dir, panel)\n", "\n", + "# mass proficient extraction (for long-term storage)\n", "if extract_prof:\n", - " # mass proficient extraction (for long-term storage)\n", - " extract_missing_fovs(base_dir, extraction_prof_dir, modify_panel_ranges(panel, start_offset=0.24, stop_offset=0.3))" + " extract_missing_fovs(base_dir, extraction_prof_dir, modify_panel_ranges(panel, start_offset=0.3, stop_offset=0.3))" ] } ],