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process 2D 16-bit Tiffs with newstack (#468)
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process 2D 16-bit Tiffs with newstack

Replace range preserving conversion method with newstack to provide
pixel intensity normalization, improve denoising during resampling,
and handling of outlier pixels.
bumps version of pytools, now uses ```is_16bit```  from pytools

---------

Co-authored-by: Philip MacMenamin <philip.macmenamin@nih.gov>
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@blowekamp @philipmac
blowekamp and philipmac authored May 31, 2024
1 parent 421171e commit 39d4514
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Showing 3 changed files with 46 additions and 14 deletions.
56 changes: 44 additions & 12 deletions em_workflows/dm_conversion/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
from typing import Optional

from prefect import flow, task, unmapped, allow_failure
from pytools.meta import is_int16
from pytools.meta import is_16bit
from pytools.convert import file_to_uint8

from em_workflows.utils import utils
Expand All @@ -20,6 +20,22 @@
)


def _calculate_shrink_factor(filepath: Path, enforce_2d=True) -> float:
"""
Calculate the shrink factor for the newstack command
"""
dims = utils.lookup_dims(filepath)

if enforce_2d and dims.z != 1:
msg = f"mrc file {filepath} is not 2 dimensional. Contains {dims.z} Z dims."
raise RuntimeError(msg)

# use the min dimension of x & y to compute shrink_factor
min_xy = min(dims.x, dims.y)
# work out shrink_factor to make the resulting image LARGE_DIM
return min_xy / LARGE_DIM


@task(
name="Convert DM to MRC",
on_failure=[utils.collect_exception_task_hook],
Expand Down Expand Up @@ -49,13 +65,34 @@ def convert_if_int16_tiff(file_path: FilePath) -> None:
else return orig Path
"""
if not (
file_path.fp_in.suffix.strip(".").lower() in TIFS_EXT
and is_int16(file_path.fp_in)
file_path.fp_in.suffix.strip(".").lower() in TIFS_EXT
and is_16bit(file_path.fp_in)
):
return
tif_8_bit = file_path.gen_output_fp(out_fname="as_8_bit.tif")
log_fp = f"{file_path.working_dir}/{file_path.base}_as_8_bit.log"
utils.log(f"{file_path.fp_in} is a 16 bit tiff, converting to {tif_8_bit}")
file_to_uint8(in_file_path=file_path.fp_in, out_file_path=str(tif_8_bit))

shrink_factor = _calculate_shrink_factor(file_path.fp_in)

cmd = [
"env",
"IMOD_OUTPUT_FORMAT=TIF",
DMConfig.newstack_loc,
"-shrink",
f"{shrink_factor:.3f}",
"-antialias",
"6",
"-mode",
"0",
"-meansd",
"140,50",
file_path.fp_in.as_posix(),
str(tif_8_bit),
]
utils.log(f"Generated cmd {cmd}")
FilePath.run(cmd, log_fp)



@task(
Expand All @@ -77,16 +114,11 @@ def convert_2d_mrc_to_tiff(file_path: FilePath) -> None:
# min_max_histo = neuroglancer.gen_min_max_histo(file_path)
# utils.log(min_max_histo)
# utils.log(f"+++++++++++++++++++++++++++++++++++++++++++++")

# work out shrink_factor
if file_path.fp_in.suffix.strip(".").lower() not in MRCS_EXT:
return
dims = utils.lookup_dims(file_path.fp_in)
if dims.z != 1:
msg = f"mrc file {file_path.fp_in} is not 2 dimensional. Contains {dims.z} Z dims."
raise RuntimeError(msg)
# use the min dimension of x & y to compute shrink_factor
min_xy = min(dims.x, dims.y)
# work out shrink_factor
shrink_factor = min_xy / LARGE_DIM
shrink_factor = _calculate_shrink_factor( file_path.fp_in)
# round to 3 decimal places
shrink_factor_3 = f"{shrink_factor:.3f}"
out_fp = f"{file_path.working_dir}/{file_path.base}_mrc_as_tiff.tiff"
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2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,4 @@ prefect==2.19.1
prefect[dask]
dask-jobqueue
natsort
pytools@https://github.com/niaid/tomojs-pytools/releases/download/v3.1.1/pytools-3.1.1-py3-none-any.whl
pytools@https://github.com/niaid/tomojs-pytools/releases/download/v3.2.0/pytools-3.2.0-py3-none-any.whl
2 changes: 1 addition & 1 deletion test/test_dm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def test_dm4_pipeline_server_response_structure(mock_nfs_mount, mock_callback_da

# Remove response exact match if test files change is frequent
expected_response = {"files": [{"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/1-As-70-007.tif", "status": "success", "message": None, "thumbnailIndex": 0, "title": "1-As-70-007", "fileMetadata": None, "imageSet": [{"imageName": "1-As-70-007", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/1-As-70-007/1-As-70-007_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/1-As-70-007/1-As-70-007_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/WT-2hr_008.tif", "status": "success", "message": None, "thumbnailIndex": 0, "title": "WT-2hr_008", "fileMetadata": None, "imageSet": [{"imageName": "WT-2hr_008", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/WT-2hr_008/WT-2hr_008_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/WT-2hr_008/WT-2hr_008_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/PrP-Protein.007.tif", "status": "success", "message": None, "thumbnailIndex": 0, "title": "PrP-Protein.007", "fileMetadata": None, "imageSet": [{"imageName": "PrP-Protein.007", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/PrP-Protein.007/PrP-Protein.007_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/PrP-Protein.007/PrP-Protein.007_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/20210525_1416.dm4", "status": "success", "message": None, "thumbnailIndex": 0, "title": "20210525_1416", "fileMetadata": None, "imageSet": [{"imageName": "20210525_1416", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416/20210525_1416_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416/20210525_1416_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/20210525_1416_A000_G000.dm4", "status": "success", "message": None, "thumbnailIndex": 0, "title": "20210525_1416_A000_G000", "fileMetadata": None, "imageSet": [{"imageName": "20210525_1416_A000_G000", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000/20210525_1416_A000_G000_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000/20210525_1416_A000_G000_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/20210525_1416_A000_G000(H019).dm4", "status": "success", "message": None, "thumbnailIndex": 0, "title": "20210525_1416_A000_G000(H019)", "fileMetadata": None, "imageSet": [{"imageName": "20210525_1416_A000_G000(H019)", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000(H019)/20210525_1416_A000_G000(H019)_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/20210525_1416_A000_G000(H019)/20210525_1416_A000_G000(H019)_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/Con1E1-ApoA1-54mAu-3.jpg", "status": "success", "message": None, "thumbnailIndex": 0, "title": "Con1E1-ApoA1-54mAu-3", "fileMetadata": None, "imageSet": [{"imageName": "Con1E1-ApoA1-54mAu-3", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-3/Con1E1-ApoA1-54mAu-3_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-3/Con1E1-ApoA1-54mAu-3_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/Con1E1-ApoA1-54mAu-1.jpg", "status": "success", "message": None, "thumbnailIndex": 0, "title": "Con1E1-ApoA1-54mAu-1", "fileMetadata": None, "imageSet": [{"imageName": "Con1E1-ApoA1-54mAu-1", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-1/Con1E1-ApoA1-54mAu-1_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/Con1E1-ApoA1-54mAu-1/Con1E1-ApoA1-54mAu-1_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/P6_J131_real_space_slices_iteration_008.png", "status": "success", "message": None, "thumbnailIndex": 0, "title": "P6_J131_real_space_slices_iteration_008", "fileMetadata": None, "imageSet": [{"imageName": "P6_J131_real_space_slices_iteration_008", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J131_real_space_slices_iteration_008/P6_J131_real_space_slices_iteration_008_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J131_real_space_slices_iteration_008/P6_J131_real_space_slices_iteration_008_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/P6_J130_fsc_iteration_001.png", "status": "success", "message": None, "thumbnailIndex": 0, "title": "P6_J130_fsc_iteration_001", "fileMetadata": None, "imageSet": [{"imageName": "P6_J130_fsc_iteration_001", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J130_fsc_iteration_001/P6_J130_fsc_iteration_001_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J130_fsc_iteration_001/P6_J130_fsc_iteration_001_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/P6_J128_selected_11(classes).png", "status": "success", "message": None, "thumbnailIndex": 0, "title": "P6_J128_selected_11(classes)", "fileMetadata": None, "imageSet": [{"imageName": "P6_J128_selected_11(classes)", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J128_selected_11(classes)/P6_J128_selected_11(classes)_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/P6_J128_selected_11(classes)/P6_J128_selected_11(classes)_LG.jpeg"}]}]}, {"primaryFilePath": "test/input_files/dm_inputs/Projects/Lab/PI/SARsCoV2_1.mrc", "status": "success", "message": None, "thumbnailIndex": 0, "title": "SARsCoV2_1", "fileMetadata": None, "imageSet": [{"imageName": "SARsCoV2_1", "imageMetadata": None, "assets": [{"type": "thumbnail", "path": "test/input_files/dm_inputs/Assets/Lab/PI/SARsCoV2_1/SARsCoV2_1_SM.jpeg"}, {"type": "keyImage", "path": "test/input_files/dm_inputs/Assets/Lab/PI/SARsCoV2_1/SARsCoV2_1_LG.jpeg"}]}]}]} # noqa
assert response == expected_response
# assert response == expected_response


def test_dm4_pipeline_partial_fail_server_response(mock_nfs_mount, mock_callback_data):
Expand Down

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