GANDLF 0.1.4.dev20250610__py3-none-any.whl → 0.1.4.dev20250612__py3-none-any.whl

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Files changed (9) hide show
  1. GANDLF/cli/generate_metrics.py +1 -1
  2. GANDLF/metrics/segmentation_panoptica.py +21 -6
  3. GANDLF/version.py +1 -1
  4. {gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/METADATA +1 -1
  5. {gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/RECORD +9 -9
  6. {gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/WHEEL +0 -0
  7. {gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/entry_points.txt +0 -0
  8. {gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/licenses/LICENSE +0 -0
  9. {gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/top_level.txt +0 -0
GANDLF/cli/generate_metrics.py CHANGED
@@ -287,7 +287,7 @@ def generate_metrics_dict(
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  pred_array = pred_tensor.squeeze(0).numpy().astype(int)
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  overall_stats_dict[current_subject_id] = generate_instance_segmentation(
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- prediction=pred_array, target=label_array
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+ prediction=pred_array, target=label_array, parameters=parameters
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  )
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  elif problem_type == "synthesis":
GANDLF/metrics/segmentation_panoptica.py CHANGED
@@ -1,4 +1,5 @@
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  from pathlib import Path
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+ import tempfile
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  import numpy as np
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@@ -6,7 +7,10 @@ from panoptica import Panoptica_Evaluator
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  def generate_instance_segmentation(
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- prediction: np.ndarray, target: np.ndarray, panoptica_config_path: str = None
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+ prediction: np.ndarray,
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+ target: np.ndarray,
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+ parameters: dict = None,
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+ panoptica_config_path: str = None,
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  ) -> dict:
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  """
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  Evaluate a single exam using Panoptica.
@@ -14,6 +18,7 @@ def generate_instance_segmentation(
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  Args:
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  prediction (np.ndarray): The input prediction containing objects.
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  label_path (str): The path to the reference label.
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+ target (np.ndarray): The input target containing objects.
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  panoptica_config_path (str): The path to the Panoptica configuration file.
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  Returns:
@@ -21,11 +26,21 @@ def generate_instance_segmentation(
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  """
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  cwd = Path(__file__).parent.absolute()
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- panoptica_config_path = (
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- cwd / "panoptica_config_brats.yaml"
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- if panoptica_config_path is None
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- else panoptica_config_path
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- )
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+ # the parameters dict takes precedence over the panoptica_config_path
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+ panoptica_config = parameters.get("panoptica_config", None)
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+ if panoptica_config is None:
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+ panoptica_config_path = (
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+ cwd / "panoptica_config_brats.yaml"
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+ if panoptica_config_path is None
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+ else panoptica_config_path
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+ )
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+ else:
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+ # write the panoptica config to a file
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+ panoptica_config_path = tempfile.NamedTemporaryFile(
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+ mode="w", delete=False, suffix=".yaml"
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+ ).name
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+ with open(panoptica_config_path, "w") as f:
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+ f.write(panoptica_config)
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  evaluator = Panoptica_Evaluator.load_from_config(panoptica_config_path)
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  # call evaluate
GANDLF/version.py CHANGED
@@ -1 +1 @@
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- __version__ = "0.1.4-dev20250610"
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+ __version__ = "0.1.4-dev20250612"
{gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: GANDLF
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- Version: 0.1.4.dev20250610
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+ Version: 0.1.4.dev20250612
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  Summary: PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.
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  Author: MLCommons
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  Author-email: gandlf@mlcommons.org
{gandlf-0.1.4.dev20250610.dist-info → gandlf-0.1.4.dev20250612.dist-info}/RECORD RENAMED
@@ -5,14 +5,14 @@ GANDLF/logger.py,sha256=oamQ1SOTTpAnC8vQ67o211Q6_bExGg_hAuqlHGlJfAI,2951
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  GANDLF/logging_config.yaml,sha256=9XxRxAKtLn5ehT1khpR8wEiJGW64sx1lylAspM5KaWk,1337
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  GANDLF/parseConfig.py,sha256=jO-ybIPxLw23OWDvFdTukbft0ZM8UOofGnoL2C5CEps,754
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  GANDLF/training_manager.py,sha256=AZlf-fl7KAwZgyre8-0M5lAyma6NvtiGX6XT51AJdxU,11436
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- GANDLF/version.py,sha256=TSEmkWJ598nnrig3HD41R2tUwAc3_g0b31QBDWk3VBc,34
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+ GANDLF/version.py,sha256=gGbVohMgfFwu60Ykq1JhAQJwAPDKpCTxPluhzigMGRw,34
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  GANDLF/anonymize/__init__.py,sha256=Nxig-jM-a-aKlK09PNi1zhNulEpLTyjnsY_oGQKdjhQ,1953
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  GANDLF/anonymize/convert_to_nifti.py,sha256=MOfSDncFGJGb-EQP9sFGn0yuKpX010Ioi2KNwttaex8,1339
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  GANDLF/cli/__init__.py,sha256=F05eyL2HKyWkHczRZuPE_Z2Yg685P9ARYxTwz6njGeQ,784
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  GANDLF/cli/config_generator.py,sha256=_j0aRV3puiIItJ1WOHRNVII_TkGJuH9ep6SuwPblcnc,4502
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  GANDLF/cli/data_split_saver.py,sha256=72ygy9s3INt2NFAfSW4j9dxxmuuvfzfBTF0Hwh0nYBU,1720
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  GANDLF/cli/deploy.py,sha256=7yPqRox6e5MB-VzHxmA4kt-W5dWwElxDm1mm019jN74,15155
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- GANDLF/cli/generate_metrics.py,sha256=CsQC8oWWEFRfZXQet_qrtTYfWn16o3jXdOh_3976GvU,20406
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+ GANDLF/cli/generate_metrics.py,sha256=ySQ5s0sGajXbr__HLOzsDtULhuZ3x7plqaC1Lz1oZto,20429
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  GANDLF/cli/huggingface_hub_handler.py,sha256=vGQYwDiT3Y8yk_xLNkB8DgW1rYpEcwYp0TCdCO5oWTs,4631
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  GANDLF/cli/main_run.py,sha256=gYNJQGvmwqBjj3ARRxj-y3R1PMOP4qTwcwFSRBbkh0k,4352
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  GANDLF/cli/patch_extraction.py,sha256=30RpBfjpwE9GLRSSD7JRqwoHngESQL0eOt09n_5r18Q,3555
@@ -111,7 +111,7 @@ GANDLF/metrics/metric_calculators.py,sha256=c-NAl84yniTWjMKePBlf0TsCIJnYHODplt8H
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  GANDLF/metrics/panoptica_config_brats.yaml,sha256=mTGSQuJoENuy84gZd2tHV0Dfl7GX5nIeE_46q5Vczx4,2685
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  GANDLF/metrics/regression.py,sha256=Ca58jo9OL1GdjB2ZvQCcrKWz9F67iY5rcbnQxT-LpcU,4584
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  GANDLF/metrics/segmentation.py,sha256=zqWEI6LuphFM0Nsm0sG2XeqAxpNJnoK1Z9q4FJt58c8,25645
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- GANDLF/metrics/segmentation_panoptica.py,sha256=ExbobmLhlyKYRKE7zEhZmuHtu5fdIUDs-53K-u4AKX8,1026
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+ GANDLF/metrics/segmentation_panoptica.py,sha256=aFGF3q_Fnf5vIWaJDMHcs2Az_fb23l2cvvifnCkgPO0,1611
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  GANDLF/metrics/synthesis.py,sha256=IfYit-R0O5ZUfmsWfLD6BqcLjjoEiotx0lUdsXWlbao,6730
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  GANDLF/models/MSDNet.py,sha256=mzBkw_kQigSDTxaR7tojhdI4ECIQ65i_qiCrNaZmBHI,3442
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  GANDLF/models/__init__.py,sha256=3SwskWonRW1AduPe6CYQWucU8ZBkkfJUpEF34I0NWP0,4286
@@ -182,9 +182,9 @@ GANDLF/utils/parameter_processing.py,sha256=DA7ZEsizWWLJZnCxBnDNh1NyA-bw5oirOvod
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  GANDLF/utils/pred_target_processors.py,sha256=aatXJ6jdJaNAHa_tPzHfC1gOQrPYJLtg-cYeUFvkM_s,2701
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  GANDLF/utils/tensor.py,sha256=AOwNTQfw9mnsomGwOF2Q_rdDS1WANlIatB0hhZN0gSg,21504
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  GANDLF/utils/write_parse.py,sha256=HROxskhet-uIdUJmz16z_7p9r0mf8hWsqQFygwZ8ap0,9202
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- gandlf-0.1.4.dev20250610.dist-info/licenses/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
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- gandlf-0.1.4.dev20250610.dist-info/METADATA,sha256=uWMTZ9ZfIKwMqRkWwoUfAw21WLGvGHSwAbHdOH7-4Tg,9932
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- gandlf-0.1.4.dev20250610.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- gandlf-0.1.4.dev20250610.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
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- gandlf-0.1.4.dev20250610.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
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- gandlf-0.1.4.dev20250610.dist-info/RECORD,,
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+ gandlf-0.1.4.dev20250612.dist-info/licenses/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
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+ gandlf-0.1.4.dev20250612.dist-info/METADATA,sha256=VmbeXSBOt1umWsVE7jgMGFgkQmZ92pisC9CST_7Ruxs,9932
187
+ gandlf-0.1.4.dev20250612.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ gandlf-0.1.4.dev20250612.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
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+ gandlf-0.1.4.dev20250612.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
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+ gandlf-0.1.4.dev20250612.dist-info/RECORD,,