Introduce `itk_infer` command by MGAMZ · Pull Request #71 · MGAMZ/ITKIT

MGAMZ · 2026-01-26T14:36:16Z

itk_infer is a CLI entry to inference samples using OneDL-MMEngine backend or ONNX backend.

Also contains modification on the deployment of pre-release to TestPyPI

📚 Documentation preview 📚: https://ITKIT--71.org.readthedocs.build/en/71/

Copilot

Pull request overview

This PR introduces a new CLI command itk_infer for batch inference on 3D medical images using either MMEngine or ONNX backends. The implementation includes sliding window inference support, multi-GPU processing, confidence scoring, and optional logits saving.

Changes:

Added new itk_infer CLI command for batch inference with MMEngine and ONNX backend support
Incremented package version from 4.0.0rc3 to 4.0.0rc4
Added verbose output to TestPyPI publishing workflow for better debugging

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
pyproject.toml	Version bump to 4.0.0rc4 and added entry point for `itk_infer` command
mkdocs.yml	Added documentation link for itk_infer in navigation menu
itkit/process/itk_infer.py	Complete implementation of batch inference tool with multi-processing support
docs/itk_infer.md	Comprehensive documentation covering usage, backends, parameters, and examples
docs/index.md	Added itk_infer to command-line tools list in main documentation page
.github/workflows/publish-to-pypi.yml	Added verbose flag to TestPyPI publishing step

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Copilot · 2026-01-26T14:41:58Z

+                confidence = calc_classwise_pred_confidence(pred_seg_logits)  # (N,)
+                pred_confidences[file.stem] = confidence[0].cpu().item()
+
+            # Save segmentation logits as .npz


Incorrect comment. The comment says "Save segmentation logits as .npz" but the code actually saves them as .zarr files (line 177). Update the comment to reflect the actual file format.

Suggested change

# Save segmentation logits as .npz

# Save segmentation logits as Zarr (.zarr)

Copilot · 2026-01-26T14:41:58Z

+    return tasks
+
+
+def set_window(image_array:np.ndarray, wl:int, ww:int) -> np.ndarray:


Missing spaces after colons in type annotations. Should be wl: int, ww: int instead of wl:int, ww:int to follow PEP 8 style guidelines and be consistent with the rest of the codebase.

Suggested change

def set_window(image_array:np.ndarray, wl:int, ww:int) -> np.ndarray:

def set_window(image_array: np.ndarray, wl: int, ww: int) -> np.ndarray:

Copilot · 2026-01-26T14:41:58Z

+    Returns:
+        confidence (Tensor): Tensor with shape (N,) representing the mean confidence across all classes.
+    """
+    assert (C:=seg_logits.size(1)) >= 2, f"Number of classes must be at least 2, got {C}."


Missing spaces around walrus operator. Should be C := seg_logits.size(1) instead of C:=seg_logits.size(1) to follow PEP 8 style guidelines and be consistent with the rest of the codebase (e.g., itkit/process/itk_patch.py:186).

Suggested change

assert (C:=seg_logits.size(1)) >= 2, f"Number of classes must be at least 2, got {C}."

assert (C := seg_logits.size(1)) >= 2, f"Number of classes must be at least 2, got {C}."

Copilot · 2026-01-26T14:41:59Z

+        p = mp.get_context('spawn').Process(
+            target = process_gpu_task,
+            args = (process_id, file_list, args, pred_conf_shared_dict),
+            daemon = True


Setting daemon=True for worker processes is problematic because daemon processes are forcibly terminated when the parent exits and cannot spawn child processes. Since the code already calls p.join() on line 265 to wait for all processes to complete, the daemon flag is unnecessary and could lead to incomplete file writes or data corruption if the parent process is interrupted. Remove the daemon=True parameter.

Suggested change

daemon = True

Copilot · 2026-01-26T14:41:59Z

+            target = process_gpu_task,
+            args = (process_id, file_list, args, pred_conf_shared_dict),
+            daemon = True


Spaces around = in keyword arguments violate PEP 8 style guidelines. According to PEP 8, keyword arguments should not have spaces around the equals sign. Change target = process_gpu_task to target=process_gpu_task, args = ... to args=..., and daemon = True to daemon=True.

Suggested change

target = process_gpu_task,

args = (process_id, file_list, args, pred_conf_shared_dict),

daemon = True

target=process_gpu_task,

args=(process_id, file_list, args, pred_conf_shared_dict),

daemon=True

Copilot · 2026-01-26T14:41:59Z

 itk_combine = "itkit.process.itk_combine:main"
 itkit-app = "itkit.gui.app:main"
 itk_slicer = "SlicerITKIT.server.itkit_server:main"
+itk_infer = "itkit.inference.itk_infer:main"


The entry point path is incorrect. The file is located at itkit/process/itk_infer.py but the entry point references itkit.inference.itk_infer:main. This will cause the command to fail at runtime with a ModuleNotFoundError. The entry point should be changed to itkit.process.itk_infer:main to match the actual file location and be consistent with other CLI commands in this project.

Suggested change

itk_infer = "itkit.inference.itk_infer:main"

itk_infer = "itkit.process.itk_infer:main"

Copilot · 2026-01-26T14:42:00Z

+    return tasks
+
+
+def set_window(image_array:np.ndarray, wl:int, ww:int) -> np.ndarray:


Missing space after colon in type annotation. Should be image_array: np.ndarray instead of image_array:np.ndarray to follow PEP 8 style guidelines and be consistent with the rest of the codebase (e.g., itkit/process/itk_extract.py:18-24).

Suggested change

def set_window(image_array:np.ndarray, wl:int, ww:int) -> np.ndarray:

def set_window(image_array: np.ndarray, wl: int, ww: int) -> np.ndarray:

Copilot · 2026-01-26T14:42:00Z

+    idx = 0
+    for i in range(args.num_proc):
+        cnt = avg + (1 if i < rem else 0)
+        tasks.append(pending[idx:idx+cnt])


Missing space around binary operator. Should be idx:idx + cnt instead of idx:idx+cnt to follow PEP 8 style guidelines.

Suggested change

tasks.append(pending[idx:idx+cnt])

tasks.append(pending[idx:idx + cnt])

Copilot · 2026-01-26T14:42:00Z

+            logits_np = pred_seg_logits[0].cpu().numpy().astype(np.float16)
+            if args.save_logits:
+                zarr.save_array(
+                    output_folder / (file.stem+'.zarr'),


Missing spaces around binary operator. Should be file.stem + '.zarr' instead of file.stem+'.zarr' to follow PEP 8 style guidelines and be consistent with the rest of the codebase.

Suggested change

output_folder / (file.stem+'.zarr'),

output_folder / (file.stem + '.zarr'),

Copilot · 2026-01-26T14:42:00Z

+import multiprocessing as mp
+import os
+import traceback
+from multiprocessing import Manager


Module 'multiprocessing' is imported with both 'import' and 'import from'.

Suggested change

from multiprocessing import Manager

codecov · 2026-01-26T14:43:56Z

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MGAMZ added 2 commits January 25, 2026 19:11

trying to fix PyPI release

dcd18f6

Introduce itk_inference

24617cf

MGAMZ self-assigned this Jan 26, 2026

Copilot AI review requested due to automatic review settings January 26, 2026 14:36

MGAMZ added the process itkit.process module label Jan 26, 2026

Copilot started reviewing on behalf of MGAMZ January 26, 2026 14:36 View session

Copilot AI reviewed Jan 26, 2026

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MGAMZ merged commit bfa8dc7 into main Jan 26, 2026
17 checks passed

MGAMZ deleted the dev/fix-testpypi branch January 26, 2026 14:44

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Introduce `itk_infer` command#71

Introduce `itk_infer` command#71
MGAMZ merged 2 commits into
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MGAMZ commented Jan 26, 2026 •

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	# Save segmentation logits as .npz
	# Save segmentation logits as Zarr (.zarr)

		return tasks


		def set_window(image_array:np.ndarray, wl:int, ww:int) -> np.ndarray:

	def set_window(image_array:np.ndarray, wl:int, ww:int) -> np.ndarray:
	def set_window(image_array: np.ndarray, wl: int, ww: int) -> np.ndarray:

	assert (C:=seg_logits.size(1)) >= 2, f"Number of classes must be at least 2, got {C}."
	assert (C := seg_logits.size(1)) >= 2, f"Number of classes must be at least 2, got {C}."

	itk_infer = "itkit.inference.itk_infer:main"
	itk_infer = "itkit.process.itk_infer:main"

	tasks.append(pending[idx:idx+cnt])
	tasks.append(pending[idx:idx + cnt])

	output_folder / (file.stem+'.zarr'),
	output_folder / (file.stem + '.zarr'),

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MGAMZ commented Jan 26, 2026 •

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