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makes find_center method to work from TomoPy #725

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Merged
dkazanc merged 3 commits into from
May 28, 2026
Merged

makes find_center method to work from TomoPy #725

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26cbebf
adds a possibility of running find_center from tomopy
dkazanc May 28, 2026
70d2c4f
cleanup small tests
dkazanc May 28, 2026
86c4fad
linting
dkazanc May 28, 2026
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4 changes: 4 additions & 0 deletions httomo/method_wrappers/rotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,8 @@ def _build_kwargs(
updated_params = {**dict_params, "ind": (dataset.shape[1] - 1) // 2}
if "average_radius" not in dict_params:
updated_params.update({"average_radius": 0})
if self.method_name == "find_center":
updated_params.update({"theta": dataset.angles_radians})
return super()._build_kwargs(updated_params, dataset)

def _gather_sino_slice(self, global_shape: Tuple[int, int, int]):
Expand Down Expand Up @@ -213,6 +215,8 @@ def _run_method(self, block: T, args: Dict[str, Any]) -> T:
args["ind"] = 0
args[self.parameters[0]] = sino_slice[:, xp.newaxis, :]
res = self.method(**args)
if isinstance(res, np.ndarray):
res = res[0]
# and broadcast
if self.comm.size > 1:
res = self.comm.bcast(res, root=0)
Expand Down
1 change: 1 addition & 0 deletions httomo/runner/task_runner.py
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Expand Up @@ -312,6 +312,7 @@ def _get_methods_name_for_snapshot(self, section: Section) -> str:
irrelevant_method_names_snapshots = [
"data_checker",
"calculate_stats",
"find_center",
"find_center_360",
"find_center_pc",
"find_center_vo",
Expand Down
162 changes: 0 additions & 162 deletions tests/test_pipeline_small.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,6 @@
import numpy as np
import pytest
from numpy.testing import assert_allclose
from PIL import Image
from plumbum import local
from .conftest import change_value_parameters_method_pipeline, check_tif

Expand Down Expand Up @@ -164,164 +163,3 @@ def test_run_pipeline_FBP3d_tomobar_denoising(
assert "Data shape is (180, 128, 160) of type uint16" in verbose_log_contents
assert "The amount of the available GPU memory is" in verbose_log_contents
assert "Using GPU 0 to transfer data of shape" in verbose_log_contents


# TODO: rewrite and move to test_pipeline_big
# @pytest.mark.small_data
# def test_tomo_standard_testing_pipeline_output_with_save_all(
# get_files: Callable,
# cmd,
# standard_data,
# standard_loader,
# testing_pipeline,
# output_folder,
# merge_yamls,
# ):
# cmd.insert(7, standard_data)
# merge_yamls(standard_loader, testing_pipeline)
# cmd.insert(8, "temp.yaml")
# cmd.insert(9, output_folder)
# subprocess.check_output(cmd)

# files = get_files("output_dir/")
# assert len(files) == 11

# _check_yaml(files, "temp.yaml")
# _check_tif(files, 3, (160, 160))

# #: check the generated h5 files
# h5_files = list(filter(lambda x: ".h5" in x, files))
# assert len(h5_files) == 5

# for file_to_open in h5_files:
# if "tomopy-recon-tomo-gridrec.h5" in file_to_open:
# with h5py.File(file_to_open, "r") as f:
# assert f["data"].shape == (160, 3, 160)
# assert f["data"].dtype == np.float32
# assert_allclose(np.mean(f["data"]), 0.0015362317, atol=1e-6, rtol=1e-6)
# assert_allclose(np.sum(f["data"]), 117.9826, atol=1e-6, rtol=1e-6)


# TODO: we will be testing this in test_pipeline_big
# def test_i12_testing_pipeline_output(
# get_files: Callable,
# cmd,
# i12_data,
# i12_loader,
# testing_pipeline,
# output_folder,
# merge_yamls,
# ):
# cmd.insert(7, i12_data)
# merge_yamls(i12_loader, testing_pipeline)
# cmd.insert(8, "temp.yaml")
# cmd.insert(9, output_folder)
# subprocess.check_output(cmd)

# files = get_files("output_dir/")
# assert len(files) == 18

# _check_yaml(files, "temp.yaml")

# log_files = list(filter(lambda x: ".log" in x, files))
# assert len(log_files) == 2

# tif_files = list(filter(lambda x: ".tif" in x, files))
# assert len(tif_files) == 10

# h5_files = list(filter(lambda x: ".h5" in x, files))
# assert len(h5_files) == 5

# gridrec_recon = list(filter(lambda x: "recon-gridrec.h5" in x, h5_files))[0]
# minus_log_tomo = list(filter(lambda x: "minus_log.h5" in x, h5_files))[0]
# remove_stripe_fw_tomo = list(
# filter(lambda x: "remove_stripe_fw.h5" in x, h5_files)
# )[0]
# normalize_tomo = list(filter(lambda x: "normalize.h5" in x, h5_files))[0]

# with h5py.File(gridrec_recon, "r") as f:
# assert f["data"].shape == (192, 10, 192)
# assert_allclose(np.sum(f["data"]), 2157.03, atol=1e-2, rtol=1e-6)
# assert_allclose(np.mean(f["data"]), 0.0058513316, atol=1e-6, rtol=1e-6)
# with h5py.File(minus_log_tomo, "r") as f:
# assert_allclose(np.sum(f["data"]), 1756628.4, atol=1e-6, rtol=1e-6)
# assert_allclose(np.mean(f["data"]), 1.2636887, atol=1e-6, rtol=1e-6)
# with h5py.File(remove_stripe_fw_tomo, "r") as f:
# assert_allclose(np.sum(f["data"]), 1766357.8, atol=1e-6, rtol=1e-6)
# assert_allclose(np.mean(f["data"]), 1.2706878, atol=1e-6, rtol=1e-6)
# with h5py.File(normalize_tomo, "r") as f:
# assert f["data"].shape == (724, 10, 192)
# assert_allclose(np.sum(f["data"]), 393510.72, atol=1e-6, rtol=1e-6)
# assert_allclose(np.mean(f["data"]), 0.28308493, atol=1e-6, rtol=1e-6)

# concise_log_file = list(filter(lambda x: "user.log" in x, files))
# concise_log_contents = _get_log_contents(concise_log_file[0])
# verbose_log_file = list(filter(lambda x: "debug.log" in x, files))
# verbose_log_contents = _get_log_contents(verbose_log_file[0])

# assert "The center of rotation is 95.5" in concise_log_contents
# assert "The full dataset shape is (724, 10, 192)" in verbose_log_contents
# assert (
# "Loading data: tests/test_data/i12/separate_flats_darks/i12_dynamic_start_stop180.nxs"
# in verbose_log_contents
# )
# assert "Path to data: /1-TempPlugin-tomo/data" in verbose_log_contents
# assert "Preview: (0:724, 0:10, 0:192)" in verbose_log_contents


# TODO: Will be added to big-data tests when the sample data with separate darks and flats will be available.
# @pytest.mark.small_data
# def test_i12_testing_ignore_darks_flats_pipeline_output(
# get_files: Callable,
# cmd,
# i12_data,
# i12_loader_ignore_darks_flats,
# testing_pipeline,
# output_folder,
# merge_yamls,
# ):
# cmd.insert(7, i12_data)
# merge_yamls(i12_loader_ignore_darks_flats, testing_pipeline)
# cmd.insert(8, "temp.yaml")
# cmd.insert(9, output_folder)
# subprocess.check_output(cmd)

# files = get_files("output_dir/")
# assert len(files) == 16

# _check_yaml(files, "temp.yaml")

# log_files = list(filter(lambda x: ".log" in x, files))
# assert len(log_files) == 1

# tif_files = list(filter(lambda x: ".tif" in x, files))
# assert len(tif_files) == 10

# h5_files = list(filter(lambda x: ".h5" in x, files))
# assert len(h5_files) == 4

# log_contents = _get_log_contents(log_files[0])
# assert "The full dataset shape is (724, 10, 192)" in log_contents
# assert (
# "Loading data: tests/test_data/i12/separate_flats_darks/i12_dynamic_start_stop180.nxs"
# in log_contents
# )
# assert "Path to data: /1-TempPlugin-tomo/data" in log_contents
# assert "Preview: (0:724, 0:10, 0:192)" in log_contents
# assert (
# "Running save_task_1 (pattern=projection): save_intermediate_data..."
# in log_contents
# )
# assert (
# "Running save_task_2 (pattern=projection): save_intermediate_data..."
# in log_contents
# )
# assert (
# "Running save_task_4 (pattern=sinogram): save_intermediate_data..."
# in log_contents
# )
# assert "The center of rotation for sinogram is 95.5" in log_contents
# assert (
# "Running save_task_5 (pattern=sinogram): save_intermediate_data..."
# in log_contents
# )
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