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prepare for evaluation phase and run more data #91

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Merged
KrisThielemans merged 6 commits into from
Sep 29, 2024
Merged

prepare for evaluation phase and run more data #91

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4e8164f
add mMR_ACR
casperdcl Aug 28, 2024
f351359
add Mediso_NEMA
casperdcl Sep 11, 2024
069f462
fine-grained metrics, skip objective
casperdcl Sep 13, 2024
73490ac
add GE_DMI3_Torso
casperdcl Sep 25, 2024
23a1699
add mMR_NEMA_lowcounts
casperdcl Sep 25, 2024
429d8f6
compute metric every 3 updates for now
KrisThielemans Sep 29, 2024
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16 changes: 12 additions & 4 deletions petric.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ class Callback(cil_callbacks.Callback):
CIL Callback but with `self.skip_iteration` checking `min(self.interval, algo.update_objective_interval)`.
TODO: backport this class to CIL.
"""
def __init__(self, interval: int = 1 << 31, **kwargs):
def __init__(self, interval: int = 1, **kwargs):
Comment thread
casperdcl marked this conversation as resolved.
super().__init__(**kwargs)
self.interval = interval

Expand Down Expand Up @@ -110,7 +110,7 @@ def __call__(self, algo: Algorithm):

class QualityMetrics(ImageQualityCallback, Callback):
"""From https://github.com/SyneRBI/PETRIC/wiki#metrics-and-thresholds"""
def __init__(self, reference_image, whole_object_mask, background_mask, interval: int = 1 << 31, **kwargs):
def __init__(self, reference_image, whole_object_mask, background_mask, interval: int = 3, **kwargs):
Comment thread
casperdcl marked this conversation as resolved.
# TODO: drop multiple inheritance once `interval` included in CIL
Callback.__init__(self, interval=interval)
ImageQualityCallback.__init__(self, reference_image, **kwargs)
Expand Down Expand Up @@ -259,10 +259,18 @@ def get_image(fname):
data_dirs_metrics = [
(SRCDIR / "Siemens_mMR_NEMA_IQ", OUTDIR / "mMR_NEMA",
[MetricsWithTimeout(outdir=OUTDIR / "mMR_NEMA", **DATA_SLICES['Siemens_mMR_NEMA_IQ'])]),
(SRCDIR / "Siemens_mMR_NEMA_IQ_lowcounts", OUTDIR / "mMR_NEMA_lowcounts",
[MetricsWithTimeout(outdir=OUTDIR / "mMR_NEMA_lowcounts", **DATA_SLICES['Siemens_mMR_NEMA_IQ_lowcounts'])]),
(SRCDIR / "NeuroLF_Hoffman_Dataset", OUTDIR / "NeuroLF_Hoffman",
[MetricsWithTimeout(outdir=OUTDIR / "NeuroLF_Hoffman", **DATA_SLICES['NeuroLF_Hoffman_Dataset'])]),
(SRCDIR / "Siemens_Vision600_thorax", OUTDIR / "Vision600_thorax",
[MetricsWithTimeout(outdir=OUTDIR / "Vision600_thorax", **DATA_SLICES['Siemens_Vision600_thorax'])])]
[MetricsWithTimeout(outdir=OUTDIR / "Vision600_thorax", **DATA_SLICES['Siemens_Vision600_thorax'])]),
(SRCDIR / "Siemens_mMR_ACR", OUTDIR / "mMR_ACR",
[MetricsWithTimeout(outdir=OUTDIR / "mMR_ACR", **DATA_SLICES['Siemens_mMR_ACR'])]),
(SRCDIR / "Mediso_NEMA_IQ", OUTDIR / "Mediso_NEMA",
[MetricsWithTimeout(outdir=OUTDIR / "Mediso_NEMA", **DATA_SLICES['Mediso_NEMA_IQ'])]),
(SRCDIR / "GE_DMI3_Torso", OUTDIR / "DMI3_Torso",
[MetricsWithTimeout(outdir=OUTDIR / "DMI3_Torso", **DATA_SLICES['GE_DMI3_Torso'])])]
else:
log.warning("Source directory does not exist: %s", SRCDIR)
data_dirs_metrics = [(None, None, [])] # type: ignore
Expand Down Expand Up @@ -293,7 +301,7 @@ def get_image(fname):
metrics_with_timeout.reset() # timeout from now
algo = Submission(data)
try:
algo.run(np.inf, callbacks=metrics + submission_callbacks)
algo.run(np.inf, callbacks=metrics + submission_callbacks, update_objective_interval=np.inf)
except Exception:
print_exc(limit=2)
finally:
Expand Down