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fix objectives.csv #53

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merged 2 commits into from
Jul 10, 2024
Merged

fix objectives.csv #53

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fa30ba7
fix objectives.csv
casperdcl Jul 10, 2024
f50765f
lint
casperdcl Jul 10, 2024
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45 changes: 25 additions & 20 deletions SIRF_data_preparation/data_QC.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,17 +19,20 @@
__version__ = '0.2.0'

import os
import os.path
import sys
from ast import literal_eval
from pathlib import Path

import matplotlib.pyplot as plt
import numpy as np
from docopt import docopt
from ast import literal_eval
from pathlib import Path
import os.path

import sirf.STIR as STIR

STIR.AcquisitionData.set_storage_scheme('memory')


def plot_sinogram_profile(prompts, background, sumaxis=(0, 1), select=0, srcdir='./'):
"""
Plot a profile through sirf.STIR.AcquisitionData
Expand All @@ -43,14 +46,10 @@ def plot_sinogram_profile(prompts, background, sumaxis=(0, 1), select=0, srcdir=
plt.plot(np.sum(prompts.as_array(), axis=sumaxis)[select, :], label='prompts')
plt.plot(np.sum(background.as_array(), axis=sumaxis)[select, :], label='background')
ax.legend()
plt.savefig(srcdir+'prompts_background_profiles.png')
plt.savefig(srcdir + 'prompts_background_profiles.png')


def plot_image(image, save_name=None,
transverse_slice=-1,
coronal_slice=-1,
sagittal_slice=-1,
vmin=0, vmax=None):
def plot_image(image, save_name=None, transverse_slice=-1, coronal_slice=-1, sagittal_slice=-1, vmin=0, vmax=None):
"""
Plot a profile through sirf.STIR.ImageData
"""
Expand All @@ -70,7 +69,7 @@ def plot_image(image, save_name=None,
plt.subplot(132)
plt.imshow(arr[:, coronal_slice, :], vmin=vmin, vmax=vmax)
plt.subplot(133)
plt.imshow(arr[:,:, sagittal_slice], vmin=vmin, vmax=vmax)
plt.imshow(arr[:, :, sagittal_slice], vmin=vmin, vmax=vmax)
plt.colorbar(shrink=.6)
if save_name is not None:
plt.savefig(save_name + '_slices.png')
Expand All @@ -85,16 +84,19 @@ def plot_image_if_exists(prefix, **kwargs):
else:
return None


def VOI_mean(image, VOI):
return float((image*VOI).sum() / VOI.sum())
return float((image * VOI).sum() / VOI.sum())


def VOI_checks(allVOInames, OSEM_image, reference_image, srcdir='.'):
if len(allVOInames) == 0:
return
OSEM_VOI_values = []
ref_VOI_values = []
for VOIname in allVOInames:
VOI = plot_image_if_exists(os.path.join(srcdir, VOIname), transverse_slice=transverse_slice, coronal_slice=coronal_slice, sagittal_slice=sagittal_slice)
VOI = plot_image_if_exists(os.path.join(srcdir, VOIname), transverse_slice=transverse_slice,
coronal_slice=coronal_slice, sagittal_slice=sagittal_slice)
if OSEM_image:
OSEM_VOI_values.append(VOI_mean(OSEM_image, VOI))
if reference_image:
Expand All @@ -114,21 +116,24 @@ def main(argv=None):
sagittal_slice = literal_eval(args['--sagittal_slice'])

if not skip_sino_profiles:
acquired_data = STIR.AcquisitionData(srcdir+'prompts.hs')
additive_term = STIR.AcquisitionData(srcdir+'additive_term.hs')
mult_factors = STIR.AcquisitionData(srcdir+'mult_factors.hs')
acquired_data = STIR.AcquisitionData(srcdir + 'prompts.hs')
additive_term = STIR.AcquisitionData(srcdir + 'additive_term.hs')
mult_factors = STIR.AcquisitionData(srcdir + 'mult_factors.hs')
background = additive_term * mult_factors
plot_sinogram_profile(acquired_data, background, srcdir=srcdir)

OSEM_image = plot_image_if_exists('OSEM_image', transverse_slice=transverse_slice, coronal_slice=coronal_slice, sagittal_slice=sagittal_slice)
plot_image_if_exists('kappa', transverse_slice=transverse_slice, coronal_slice=coronal_slice, sagittal_slice=sagittal_slice)
reference_image = plot_image_if_exists(srcdir + 'PETRIC/reference_image', transverse_slice=transverse_slice, coronal_slice=coronal_slice, sagittal_slice=sagittal_slice)
OSEM_image = plot_image_if_exists('OSEM_image', transverse_slice=transverse_slice, coronal_slice=coronal_slice,
sagittal_slice=sagittal_slice)
plot_image_if_exists('kappa', transverse_slice=transverse_slice, coronal_slice=coronal_slice,
sagittal_slice=sagittal_slice)
reference_image = plot_image_if_exists(srcdir + 'PETRIC/reference_image', transverse_slice=transverse_slice,
coronal_slice=coronal_slice, sagittal_slice=sagittal_slice)

VOIdir = os.path.join(srcdir, srcdir + "PETRIC")
allVOInames = [ os.path.basename(str(voi)[:-3]) for voi in Path(VOIdir).glob("VOI_*.hv")]
allVOInames = [os.path.basename(str(voi)[:-3]) for voi in Path(VOIdir).glob("VOI_*.hv")]
VOI_checks(allVOInames, OSEM_image, reference_image, srcdir=VOIdir)
plt.show()


if __name__ == '__main__':
main()

13 changes: 4 additions & 9 deletions petric.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,7 @@
TEAM = os.getenv("GITHUB_REPOSITORY", "SyneRBI/PETRIC-").split("/PETRIC-", 1)[-1]
VERSION = os.getenv("GITHUB_REF_NAME", "")
OUTDIR = Path(f"/o/logs/{TEAM}/{VERSION}" if TEAM and VERSION else "./output")
SRCDIR = Path("/mnt/share/petric")
if not SRCDIR.is_dir():
if not (SRCDIR := Path("/mnt/share/petric")).is_dir():
SRCDIR = Path("./data")


Expand All @@ -52,7 +51,7 @@ def __call__(self, algo: Algorithm):
if algo.iteration % algo.update_objective_interval == 0 or algo.iteration == algo.max_iteration:
log.debug("saving iter %d...", algo.iteration)
algo.x.write(str(self.outdir / f'iter_{algo.iteration:04d}.hv'))
self.csv.writerow((algo.iterations, algo.loss))
self.csv.writerow((algo.iteration, algo.get_last_loss()))
log.debug("...saved")
if algo.iteration == algo.max_iteration:
algo.x.write(str(self.outdir / 'iter_final.hv'))
Expand Down Expand Up @@ -161,11 +160,7 @@ def construct_RDP(penalty_strength, initial_image, kappa, max_scaling=1e-3):
initial_image: used to determine a smoothing factor (epsilon).
kappa: used to pass voxel-dependent weights.
"""
try:
prior = STIR.CudaRelativeDifferencePrior()
except NameError:
prior = STIR.RelativeDifferencePrior()

prior = getattr(STIR, 'CudaRelativeDifferencePrior', STIR.RelativeDifferencePrior)()
# need to make it differentiable
epsilon = initial_image.max() * max_scaling
prior.set_epsilon(epsilon)
Expand Down Expand Up @@ -229,7 +224,7 @@ def get_image(fname):
[MetricsWithTimeout(outdir=OUTDIR / "Vision600_thorax")])]
else:
log.warning("Source directory does not exist: %s", SRCDIR)
data_dirs_metrics = [(None, None, [])]
data_dirs_metrics = [(None, None, [])] # type: ignore

if __name__ != "__main__":
# load up first data-set for people to play with
Expand Down