remove unused arguments

AllenCell · Nov 27, 2024 · aab2e64 · aab2e64
1 parent 4797ca3
commit aab2e64
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Showing 3 changed files with 0 additions and 58 deletions.
diff --git a/subpackages/image_preprocessing/config/step/one_step.yaml b/subpackages/image_preprocessing/config/step/one_step.yaml
@@ -5,52 +5,11 @@ step:
   _target_: image_preprocessing.steps.OneStep
   raw_col: crop_raw
   seg_col: crop_seg
-  fov_col: fov_path
   channel_map_col: name_dict
-  roi_col: roi
   alignment_channel: dna_segmentation
   membrane_seg_channel: dna_segmentation
-  mask_map:
-    bf: membrane_segmentation
-    dna: membrane_segmentation
-    membrane: membrane_segmentation
-    structure: membrane_segmentation
-
   dilation_shape: null
   make_unique: false
-
-  clip_quantile: 0.975
-  quantile: 0.95
-  output_format: ome.zarr
-  downscale_num_levels: 4
-  downscale_factor: 2.0
-  structure_clip_values:
-    FBL: [420, 2610]
-    NPM1: [480, 8300]
-    SON: [420, 1500]
-    SMC1A: [450, 630]
-    HIST1H2BJ: [450, 2885]
-    LMNB1: [475, 1700]
-    NUP153: [420, 600]
-    SEC61B: [490, 1070]
-    ATP2A2: [430, 670]
-    SLC25A17: [400, 515]
-    RAB5A: [420, 600]
-    TOMM20: [410, 815]
-    LAMP1: [440, 800]
-    ST6GAL1: [400, 490]
-    TUBA1B: [1100, 3200]
-    CETN2: [440, 800]
-    GJA1: [420, 2200]
-    TJP1: [420, 1500]
-    DSP: [410, 620]
-    CTNNB1: [410, 750]
-    AAVS1: [505, 2255]
-    ACTB: [550, 1300]
-    ACTN1: [440, 730]
-    MYH10: [440, 900]
-    PXN: [410, 490]
-
   output_dir: ${output_dir}/one_step
 
 input: ${input_manifest}
diff --git a/subpackages/image_preprocessing/config/step/register.yaml b/subpackages/image_preprocessing/config/step/register.yaml
@@ -6,9 +6,6 @@ step:
   input_col: aligned_image
   quantile: 0.95
   membrane_seg_channel: membrane_segmentation
-  output_format: ome.zarr
-  downscale_num_levels: 4
-  downscale_factor: 2.0
   output_dir: ${output_dir}/register
 
 input: ${output_dir}/align/manifest.parquet
diff --git a/subpackages/image_preprocessing/image_preprocessing/steps/one_step.py b/subpackages/image_preprocessing/image_preprocessing/steps/one_step.py
@@ -46,37 +46,23 @@ def __init__(
         self,
         raw_col,
         seg_col,
-        fov_col,
         channel_map_col,
-        roi_col,
         alignment_channel,
-        mask_map,
         dilation_shape,
-        quantile,
         make_unique=False,
         membrane_seg_channel="membrane_segmentation",
-        padding=0,
-        structure_clip_values=dict(),
-        clip_quantile=0.975,
         **kwargs,
     ):
         super().__init__(**kwargs)
         self.raw_col = raw_col
         self.seg_col = seg_col
-        self.fov_col = fov_col
         self.channel_map_col = channel_map_col
-        self.roi_col = roi_col
         self.alignment_channel = alignment_channel
         self.make_unique = make_unique
-        self.mask_map = mask_map
         self.binary_structure = (
             np.ones(dilation_shape) if dilation_shape is not None else None
         )
         self.membrane_seg_channel = membrane_seg_channel
-        self.padding = padding
-        self.structure_clip_values = structure_clip_values
-        self.clip_quantile = clip_quantile
-        self.quantile = quantile
 
     def run_step(self, row):
         cell_id = row[self.cell_id_col]