Merge pull request #167 from mehta-lab/bkg-correction-fixes2

Fix background correction for non-square images and online mode

recOrder/io/utils.py

@@ -72,7 +72,7 @@ def load_bg(bg_path, height, width, ROI=None):
  for i in range(len(bg_paths)):
  img = tiff.imread(bg_paths[i])
 
- if ROI is not None and ROI != (0, 0, height, width):
+ if ROI is not None and ROI != (0, 0, width, height):
  bg_data[i, :, :] = np.mean(img[ROI[1]:ROI[1] + ROI[3], ROI[0]:ROI[0] + ROI[2]])
 
  else:
@@ -165,3 +165,21 @@ def get_unimodal_threshold(input_image):
  max_dist = per_dist
  assert best_threshold > -np.inf, 'Error in unimodal thresholding'
  return best_threshold
+def rec_bkg_to_wo_bkg(recorder_option) -> str:
+ """
+ Converts recOrder's background options to waveorder's background options.
+
+ Parameters
+ ----------
+ recorder_option
+
+ Returns
+ -------
+ waveorder_option
+
+ """
+ if recorder_option == 'local_fit+':
+ return 'local_fit'
+ else:
+ return recorder_option
+

recOrder/pipelines/qlipp_pipeline.py

@@ -2,7 +2,7 @@
 from waveorder.io.reader import WaveorderReader
 from waveorder.io.writer import WaveorderWriter
 from recOrder.io import MetadataReader
-from recOrder.io.utils import load_bg, MockEmitter
+from recOrder.io.utils import load_bg, MockEmitter, rec_bkg_to_wo_bkg
 from recOrder.compute.qlipp_compute import reconstruct_qlipp_birefringence, reconstruct_qlipp_stokes, \
  reconstruct_phase2D, reconstruct_phase3D, initialize_reconstructor
 import numpy as np
@@ -72,11 +72,7 @@ def __init__(self, config: ConfigReader, data: WaveorderReader, writer: Waveorde
  self.data_shape = (self.t, len(self.output_channels), self.slices, self.img_dim[0], self.img_dim[1])
  self.chunk_size = (1, 1, 1, self.data_shape[-2], self.data_shape[-1])
 
- # Convert 'local_fit+' to 'local_fit' for waveorder
- if self.config.background_correction == 'local_fit+':
- wo_background_correction = 'local_fit'
- else:
- wo_background_correction = self.config.background_correction
+ wo_background_correction = rec_bkg_to_wo_bkg(self.config.background_correction)
 
  # Initialize Reconstructor
  if self.no_phase:
@@ -122,7 +118,6 @@ def __init__(self, config: ConfigReader, data: WaveorderReader, writer: Waveorde
  else:
  self.bg_stokes = None
 
-
  def _check_output_channels(self, output_channels):
  self.no_birefringence = True
  self.no_phase = True

recOrder/plugin/widget/main_widget.py

@@ -769,7 +769,7 @@ def _check_requirements_for_acq(self, mode):
  raise_error = True
  self._set_tab_red('General', True)
 
- if self.bg_option == 'local_fit' or self.bg_option == 'local_fit+' or self.bg_option == 'Global':
+ if self.bg_option == 'local_fit' or self.bg_option == 'local_fit+' or self.bg_option == 'global':
  success = self._check_line_edit('bg_path')
  if not success:
  raise_error = True
@@ -1376,7 +1376,7 @@ def _populate_from_config(self):
  self.bg_option = self.config_reader.background_correction
  if self.bg_option == 'None':
  self.ui.cb_bg_method.setCurrentIndex(0)
- elif self.bg_option == 'Global':
+ elif self.bg_option == 'global':
  self.ui.cb_bg_method.setCurrentIndex(1)
  elif self.bg_option == 'local_fit':
  self.ui.cb_bg_method.setCurrentIndex(2)
@@ -2117,7 +2117,7 @@ def enter_bg_correction(self):
  self.ui.label_bg_path.setHidden(False)
  self.ui.le_bg_path.setHidden(False)
  self.ui.qbutton_browse_bg_path.setHidden(False)
- self.bg_option = 'Global'
+ self.bg_option = 'global'
  elif state == 2:
  self.ui.label_bg_path.setHidden(True)
  self.ui.le_bg_path.setHidden(True)

recOrder/plugin/workers/acquisition_workers.py

@@ -8,6 +8,7 @@
  deconvolve_fluorescence_2D, calculate_background
 from recOrder.io.zarr_converter import ZarrConverter
 from recOrder.io.metadata_reader import MetadataReader, get_last_metadata_file
+from recOrder.io.utils import rec_bkg_to_wo_bkg
 from napari.qt.threading import WorkerBaseSignals, WorkerBase
 import logging
 from waveorder.io.writer import WaveorderWriter
@@ -959,6 +960,8 @@ def _reconstruct(self, stack):
 
  self._check_abort()
 
+ wo_background_correction = rec_bkg_to_wo_bkg(self.calib_window.bg_option)
+
  # Initialize the heavy reconstuctor
  if self.mode == 'phase' or self.mode == 'all':
 
@@ -981,7 +984,7 @@ def _reconstruct(self, stack):
  z_step_um=self.calib_window.z_step,
  pad_z=self.calib_window.pad_z,
  pixel_size_um=self.calib_window.ps,
- bg_correction=self.calib_window.bg_option,
+ bg_correction=wo_background_correction,
  n_obj_media=self.calib_window.n_media,
  mode=self.calib_window.phase_dim,
  use_gpu=self.calib_window.use_gpu,
@@ -1010,7 +1013,7 @@ def _reconstruct(self, stack):
  z_step_um=self.calib_window.z_step,
  pad_z=self.calib_window.pad_z,
  pixel_size_um=self.calib_window.ps,
- bg_correction=self.calib_window.bg_option,
+ bg_correction=wo_background_correction,
  n_obj_media=self.calib_window.n_media,
  mode=self.calib_window.phase_dim,
  use_gpu=self.calib_window.use_gpu,
@@ -1033,11 +1036,12 @@ def _reconstruct(self, stack):
  calibration_scheme=self.calib_window.calib_scheme,
  wavelength_nm=self.calib_window.wavelength,
  swing=self.calib_window.swing,
- bg_correction=self.calib_window.bg_option,
+ bg_correction=wo_background_correction,
  n_slices=self.n_slices)
 
- # Check to see if background correction is desired and compute BG stokes
- if self.calib_window.bg_option != 'None':
+ # Prepare background corrections for waveorder
+ # This block mimics qlipp_pipeline.py L110-119.
+ if self.calib_window.bg_option in ['global', 'local_fit+']:
  logging.debug('Loading BG Data')
  self._check_abort()
  bg_data = self._load_bg(self.calib_window.acq_bg_directory, stack.shape[-2], stack.shape[-1])
@@ -1046,6 +1050,9 @@ def _reconstruct(self, stack):
  self._check_abort()
  bg_stokes = recon.Stokes_transform(bg_stokes)
  self._check_abort()
+ elif self.calib_window.bg_option == 'local_fit':
+ bg_stokes = np.zeros((5, stack.shape[-2], stack.shape[-1]))
+ bg_stokes[0, ...] = 1 # Set background to "identity" Stokes parameters.
  else:
  logging.debug('No Background Correction method chosen')
  bg_stokes = None