Revert back to old deficient and proficient extraction ranges

angelolab · Aug 15, 2023 · 91c7d9e · 91c7d9e
1 parent e6f70cb
commit 91c7d9e
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Showing 2 changed files with 8 additions and 10 deletions.
diff --git 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
@@ -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))"
  ]
  }
  ],