Merge branch 'main' into SAGA

.gitignore

@@ -1,5 +1,6 @@
 data/
 orgdata/
+orgdata
 output/
 tmp*/
 err*.txt
@@ -13,3 +14,6 @@ __pycache__/
 *.ahv
 *.hv
 *.v
+*.csv
+# Tensorboard files
+events.*

SIRF_data_preparation/Mediso_NEMA_IQ/README.md

@@ -0,0 +1,36 @@
+# Data from the Mediso AnyScan at NPL
+Initial processing steps
+```sh
+orgpath=/mnt/share/petric-wip/NEMA_Challenge
+#orgpath=~/devel/PETRIC/orgdata/
+# cd $orgpath
+#wget https://nplanywhere.npl.co.uk/userportal/?v=4.6.1#/shared/public/nrKe5vWynvyMsp7m/e9e3d4b8-8f83-47be-bf2d-17a96a7a8aac
+#unzip NEMA_Challenge.zip
+cd ~/devel/PETRIC/data
+mkdir -p  Mediso_NEMA_IQ
+cd Mediso_NEMA_IQ/
+# trim sinograms to avoid "corner" problems in mult_factors
+# TODO for next data: use 30 (as some problems remain)
+for f in additive_term.hs  mult_factors.hs  prompts.hs; do
+   SSRB -t 20 $f $orgpath/sinograms/$f
+done
+# alternative if we don't need to trim
+#cp -rp $orgpath/sinograms/* .
+# get rid of NaNs
+python prepare.py
+# now handle VOIs
+mkdir PETRIC
+cp -rp $orgpath/VOIs/* PETRIC
+# cp -rp $orgpath/README.md .
+cd PETRIC
+stir_math VOI_background.hv VOI_backgroung.hv
+rm VOI_backgroung.*
+rm *ahv
+cd ..
+python ../../SIRF_data_preparation/create_initial_images.py --template_image=PETRIC/VOI_whole_object.hv .
+ ```
+ I needed to fix the OSEM header (manual):
+ ```
+ !imaging modality := PT
+ ```
+python ../../SIRF_data_preparation/data_QC

SIRF_data_preparation/Mediso_NEMA_IQ/prepare.py

@@ -0,0 +1,11 @@
+# Set NaNs to zero in additive_term
+import numpy as np
+
+import sirf.STIR
+
+additive = sirf.STIR.AcquisitionData('additive_term.hs')
+add_arr = additive.as_array()
+add_arr = np.nan_to_num(add_arr)
+new_add = additive.clone()
+new_add.fill(add_arr)
+new_add.write('additive_term.hs')

SIRF_data_preparation/README.md

@@ -25,3 +25,38 @@ for the Siemens mMR NEMA IQ data (on Zenodo):
 - `download_Siemens_mMR_NEMA_IQ.py`: download and extract
 - `prepare_mMR_NEMA_IQ_data.py`: prepare the data (prompts etc)
 - `BSREM_*.py`: functions with specific settings for a particular data-set
+
+# Steps to follow to prepare data
+If starting from Siemens list-mode data and letting SIRF take care of scatter etc, check for instance [Siemens_mMR_ACR/README.md](steps for Siemens mMR ACR). If pre-prepared data are given, check that naming of all files is correct. KT normally puts all data
+in `~/devel/PETRIC/data/<datasetname>` with `datasetname` following convention of `scanner_phantom-name` as others (instructions below and indeed some scripts might assume this location). Change working directory to where data sits and add PETRIC to your python-path, e.g.
+```
+PYTHONPATH=~/devel/PETRIC:$PYTHONPATH`
+```
+
+1. Run initial [data_QC.py](data_QC.py)
+   ```
+   python -m SIRF_data_preparation.data_QC
+   ```
+
+2. Run [create_initial_images.py](create_initial_images.py).
+   ```
+   python -m SIRF_data_preparation.create_initial_images --template_image=<some_image>
+   ```
+   where the template image is one of the given VOIs (it does not matter which one, as they should all have the same geometry). (If you need to create VOIs yourself, you can use `None` or the vendor image).
+3. Edit `OSEM_image.hv` to add modality, radionuclide and duration info which got lost (copy from `prompts.hs`)
+4. Edit [dataset_settings.py](dataset_settings.py) for subsets (used by our reference reconstructions only, not by participants).
+5. Edit [petric.py](../petric.py) for slices to use for creating figures (`DATA_SLICES`). Note that `data_QC` outputs centre-of-mass of the VOIs, which can be helpful for this.
+6. Run [data_QC.py](data_QC.py) which should now make more plots. Check VOI alignment etc.
+   ```
+   python -m SIRF_data_preparation.data_QC --dataset=<datasetname>
+   ```
+7. `cd ../..`
+8. `python -m SIRF_data_preparation.run_OSEM <datasetname>`
+9. `python -m SIRF_data_preparation.run_BSREM  <datasetname>`
+10. Adapt [plot_BSREM_metrics.py](plot_BSREM_metrics.py) (probably only the `<datasetname>`) and run interactively.
+11. Copy the BSREM ` iter_final` to `data/<datasetname>/PETRIC/reference_image`, e.g.
+    ```
+    stir_math data/<datasetname>/PETRIC/reference_image.hv output/<datasetname>/iter_final.hv
+    ```
+12. `cd data/<datasetname>; rm -f *ahv info.txt warnings.txt`, check its `README.md` etc
+13. Transfer to web-server

SIRF_data_preparation/Siemens_mMR_ACR/README.md

@@ -4,7 +4,7 @@ ugly and temporary
 Steps to follow:
 1. `python SIRF_data_preparation/Siemens_mMR_ACR/download.py`
 2. `python SIRF_data_preparation/Siemens_mMR_ACR/prepare.py` (As there is no useful mumap, this will **not** do attenuation and scatter estimation)
-3. `python SIRF_data_preparation/create_initial_images.py data/Siemens_mMR_ACR/final --template_image=None` (Reconstruct at full FOV size)
+3. `python SIRF_data_preparation.create_initial_images data/Siemens_mMR_ACR/final --template_image=None` (Reconstruct at full FOV size)
 4. `mv data/Siemens_mMR_ACR/final/OSEM_image.* data/Siemens_mMR_ACR/processing` (this is really an NAC image and ideally would be renamed)
 5. `python SIRF_data_preparation/Siemens_mMR_ACR/register_mumap.py` (output is orgdata/Siemens_mMR_ACR/processing/reg_mumap.hv etc)
 6. However, registration failed, so this needs a manual intervention step:
@@ -24,9 +24,9 @@ Steps to follow:
    stir_math --accumulate  orgdata/Siemens_mMR_ACR/processing/reg_mumap.hv  orgdata/Siemens_mMR_ACR/output/ACR_hardware-to-STIR.nii.gz
    ```
 7. 11. `python SIRF_data_preparation/run_OSEM.py Siemens_mMR_ACR`--end 200` (As there is now a useful mumap, this will now do attenuation and scatter estimation)
-8. `python SIRF_data_preparation/create_initial_images.py data/Siemens_mMR_ACR --template_image=../../orgdata/Siemens_mMR_ACR/output/sampling_masks/acr-all-sampling-0-2mm_dipy.nii`
-9. `python SIRF_data_preparation/data_QC.py --srcdir='data/Siemens_mMR_ACR' --transverse_slice=99`
-10. edit `SIRF_data_prepatation/dataset_settings.py` for subsets etc. edit `OSEM_image.hv` to add modality, radionuclide and duration info which got lost.
+8. `python -m SIRF_data_preparation.create_initial_images data/Siemens_mMR_ACR --template_image=../../orgdata/Siemens_mMR_ACR/output/sampling_masks/acr-all-sampling-0-2mm_dipy.nii`
+9. `python -m SIRF_data_preparation.data_QC --srcdir='data/Siemens_mMR_ACR' --transverse_slice=99`
+10. edit `petric.py` and `SIRF_data_preparation/dataset_settings.py` for subsets etc. edit `OSEM_image.hv` to add modality, radionuclide and duration info which got lost.
 11. `python SIRF_data_preparation/Siemens_mMR_ACR/VOI_prep.py`
 12. `python SIRF_data_preparation/run_OSEM.py Siemens_mMR_ACR`
 13. `python SIRF_data_preparation/run_BSREM.py Siemens_mMR_ACR`

SIRF_data_preparation/Siemens_mMR_ACR/prepare.py

@@ -2,7 +2,7 @@
 import logging
 import os
 
-from SIRF_data_preparation.data_utilities import prepare_challenge_Siemens_data, the_data_path, the_orgdata_path
+from ..data_utilities import prepare_challenge_Siemens_data, the_data_path, the_orgdata_path
 
 scanID = 'Siemens_mMR_ACR'
 

SIRF_data_preparation/Siemens_mMR_NEMA_IQ/prepare_mMR_NEMA_IQ_data.py

@@ -2,7 +2,7 @@
 import logging
 import os
 
-from .data_utilities import prepare_challenge_Siemens_data, the_data_path
+from ..data_utilities import prepare_challenge_Siemens_data, the_data_path, the_orgdata_path
 
 this_directory = os.path.dirname(__file__)
 repo_directory = os.path.dirname(this_directory)

SIRF_data_preparation/Siemens_mMR_NEMA_IQ_lowcounts/README.md

@@ -0,0 +1,8 @@
+# Siemens mMR NEMA IQ data (low counts)
+
+This relies on the "normal" count level processsing to be done first, specifically the download and the ROIs.
+
+Steps to follow:
+1. `prepare_mMR_NEMA_IQ_data.py`
+2. copy VOIs
+3. further steps as [normal](../README.md#steps-to-follow-to-prepare-data)

SIRF_data_preparation/Siemens_mMR_NEMA_IQ_lowcounts/prepare_mMR_NEMA_IQ_data.py

@@ -0,0 +1,48 @@
+import argparse
+import logging
+import os
+
+from ..data_utilities import prepare_challenge_Siemens_data, the_data_path, the_orgdata_path
+
+this_directory = os.path.dirname(__file__)
+repo_directory = os.path.dirname(this_directory)
+challenge_data_path = os.path.join(repo_directory, 'data')
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='SyneRBI PETRIC Siemens mMR NEMA IQ data preparation script.')
+
+    parser.add_argument('--log', type=str, default='warning')
+    parser.add_argument('--start', type=float, default=0)
+    parser.add_argument('--end', type=float, default=100)
+    parser.add_argument('--raw_data_path', type=str, default=None)
+    args = parser.parse_args()
+
+    if args.log in ['debug', 'info', 'warning', 'error', 'critical']:
+        level = eval(f'logging.{args.log.upper()}')
+        logging.basicConfig(level=level)
+        logging.info(f"Setting logging level to {args.log.upper()}")
+
+    start = args.start
+    end = args.end
+
+    if args.raw_data_path is None:
+        data_path = the_orgdata_path('Siemens_mMR_NEMA_IQ', 'raw', 'NEMA_IQ')
+    else:
+        data_path = args.raw_data_path
+
+    data_path = os.path.abspath(data_path)
+    logging.debug(f"Raw data path: {data_path}")
+
+    intermediate_data_path = the_orgdata_path('Siemens_mMR_NEMA_IQ_lowcounts', 'processing')
+    challenge_data_path = the_data_path('Siemens_mMR_NEMA_IQ_lowcounts')
+
+    os.makedirs(challenge_data_path, exist_ok=True)
+    os.chdir(challenge_data_path)
+    os.makedirs(intermediate_data_path, exist_ok=True)
+
+    f_template = os.path.join(data_path, 'mMR_template_span11.hs')
+
+    prepare_challenge_Siemens_data(data_path, challenge_data_path, intermediate_data_path, '20170809_NEMA_',
+                                   '60min_UCL.l.hdr', 'MUMAP_UCL.v', 'MUMAP_UCL.hv', 'UCL.n', 'norm.n.hdr', f_template,
+                                   'prompts', 'mult_factors', 'additive_term', 'randoms', 'attenuation_factor',
+                                   'attenuation_correction_factor', 'scatter', start, end)

SIRF_data_preparation/create_initial_images.py

@@ -8,15 +8,15 @@
 
 Options:
   -t <template_image>, --template_image=<template_image>  filename (relative to <data_path>) of image to use
-                                                          for data sizes [default: PETRIC/VOI_whole_phantom.hv]
+                                                          for data sizes [default: PETRIC/VOI_whole_object.hv]
   -s <xy-size>, --xy-size=<xy-size>  force xy-size (do not use when using VOIs as init) [default: -1]
   -S <subsets>, --subsets=<subsets>  number of subsets [default: 2]
   -i <subiterations>, --subiterations=<subiterations>     number of sub-iterations [default: 14]
 """
 # Copyright 2024 Rutherford Appleton Laboratory STFC
 # Copyright 2024 University College London
 # Licence: Apache-2.0
-__version__ = '0.1.0'
+__version__ = '0.2.0'
 
 import logging
 import math
@@ -82,9 +82,8 @@ def compute_kappa_image(obj_fun, initial_image):
 
     WARNING: Assumes the objective function has been set-up already
     """
-    # This needs SIRF 3.7. If you don't have that yet, you should probably upgrade anyway!
-    Hessian_row_sum = obj_fun.multiply_with_Hessian(initial_image, initial_image.allocate(1))
-    return (-1 * Hessian_row_sum).power(.5)
+    minus_Hessian_row_sum = -1 * obj_fun.multiply_with_Hessian(initial_image, initial_image.allocate(1))
+    return minus_Hessian_row_sum.maximum(0).power(.5)
 
 
 def main(argv=None):

SIRF_data_preparation/data_QC.py

@@ -6,17 +6,18 @@
 
 Options:
   -h, --help
-  --srcdir=<path>        pathname (must have trailing slash!) [default: ./]
+  --srcdir=<path>        pathname. Will default to current directory unless dataset is set
   --skip_sino_profiles   do not plot the sinogram profiles
   --transverse_slice=<i>  idx [default: -1]
   --coronal_slice=<c>    idx [default: -1]
   --sagittal_slice=<s>   idx [default: -1]
+  --dataset=<name>       dataset name. if set, it is used to override default slices
 
 Note that -1 one means to use middle of image
 """
 # Copyright 2024 University College London
 # Licence: Apache-2.0
-__version__ = '0.2.0'
+__version__ = '0.4.0'
 
 import os
 import os.path
@@ -29,6 +30,8 @@
 from scipy import ndimage
 
 import sirf.STIR as STIR
+from SIRF_data_preparation.dataset_settings import get_settings
+from SIRF_data_preparation.data_utilities import the_data_path
 
 STIR.AcquisitionData.set_storage_scheme('memory')
 
@@ -119,7 +122,10 @@ def VOI_checks(allVOInames, OSEM_image=None, reference_image=None, srcdir='.', *
             print(f"VOI {VOIname} does not exist")
             continue
         VOI = STIR.ImageData(filename)
-        COM = np.rint(ndimage.center_of_mass(VOI.as_array()))
+        VOI_arr = VOI.as_array()
+        COM = np.rint(ndimage.center_of_mass(VOI_arr))
+        num_voxels = VOI_arr.sum()
+        print(f"VOI: {VOIname}: COM (in indices): {COM} voxels {num_voxels} = {num_voxels * np.prod(VOI.spacing)} mm^3")
         plt.figure()
         plot_image(VOI, save_name=prefix, vmin=0, vmax=1, transverse_slice=int(COM[0]), coronal_slice=int(COM[1]),
                    sagittal_slice=int(COM[2]))
@@ -149,13 +155,25 @@ def VOI_checks(allVOInames, OSEM_image=None, reference_image=None, srcdir='.', *
 
 def main(argv=None):
     args = docopt(__doc__, argv=argv, version=__version__)
+    dataset = args['--dataset']
     srcdir = args['--srcdir']
     skip_sino_profiles = args['--skip_sino_profiles']
     slices = {}
     slices["transverse_slice"] = literal_eval(args['--transverse_slice'])
     slices["coronal_slice"] = literal_eval(args['--coronal_slice'])
     slices["sagittal_slice"] = literal_eval(args['--sagittal_slice'])
 
+    if (dataset):
+        if srcdir is None:
+            srcdir = the_data_path(dataset)
+        settings = get_settings(dataset)
+        for key in slices.keys():
+            if slices[key] == -1 and key in settings.slices:
+                slices[key] = settings.slices[key]
+    else:
+        if srcdir is None:
+            srcdir = os.getcwd()
+
     if not skip_sino_profiles:
         acquired_data = STIR.AcquisitionData(os.path.join(srcdir, 'prompts.hs'))
         additive_term = STIR.AcquisitionData(os.path.join(srcdir, 'additive_term.hs'))

SIRF_data_preparation/dataset_settings.py

@@ -1,7 +1,12 @@
 """Settings for recon and display used in the data preparation"""
-
 from dataclasses import dataclass
 
+from petric import DATA_SLICES
+
+DATA_SUBSETS = {
+    'Siemens_mMR_NEMA_IQ': 7, 'Siemens_mMR_NEMA_IQ_lowcounts': 7, 'Siemens_mMR_ACR': 7, 'NeuroLF_Hoffman_Dataset': 16,
+    'Mediso_NEMA_IQ': 12, 'Siemens_Vision600_thorax': 5}
+
 
 @dataclass
 class DatasetSettings:
@@ -10,16 +15,4 @@ class DatasetSettings:
 
 
 def get_settings(scanID: str):
-    if scanID == 'Siemens_mMR_NEMA_IQ':
-        slices = {'transverse_slice': 72, 'coronal_slice': 109} # , 'sagittal_slice': 89}
-        num_subsets = 7
-    elif scanID == 'Siemens_mMR_ACR':
-        slices = {'transverse_slice': 99}
-        num_subsets = 7
-    elif scanID == 'NeuroLF_Hoffman_Dataset':
-        slices = {'transverse_slice': 72}
-        num_subsets = 16
-    else:                                                       # Vision
-        slices = {}
-        num_subsets = 5
-    return DatasetSettings(num_subsets, slices)
+    return DatasetSettings(DATA_SUBSETS[scanID], DATA_SLICES[scanID])

SIRF_data_preparation/plot_BSREM_metrics.py

@@ -1,4 +1,5 @@
-"""Preliminary file to check evolution of metrics as well as pass_index"""
+# %%
+# """Preliminary file to check evolution of metrics as well as pass_index"""
 # %load_ext autoreload
 # %autoreload 2
 from pathlib import Path
@@ -21,7 +22,8 @@
 
 # scanID = 'Siemens_Vision600_thorax'
 # scanID = 'NeuroLF_Hoffman_Dataset'
-scanID = 'Siemens_mMR_NEMA_IQ'
+# scanID = 'Siemens_mMR_NEMA_IQ'
+scanID = 'Mediso_NEMA_IQ'
 
 srcdir = SRCDIR / scanID
 outdir = OUTDIR / scanID
@@ -69,16 +71,19 @@
     reference_image = STIR.ImageData(str(datadir / 'iter_final.hv'))
 qm = QualityMetrics(reference_image, data.whole_object_mask, data.background_mask, tb_summary_writer=None,
                     voi_mask_dict=data.voi_masks)
+# %% get update ("iteration") numbers from objective functions
 last_iteration = int(objs[-1, 0] + .5)
-iteration_interval = int(objs[-1, 0] - objs[-2, 0] + .5)
+# find interval(don't use last value, as that interval can be smaller)
+iteration_interval = int(objs[-2, 0] - objs[-3, 0] + .5)
 if datadir1.is_dir():
     last_iteration = int(objs0[-1, 0] + .5)
     iteration_interval = int(objs0[-1, 0] - objs0[-2, 0] + .5) * 2
 # %%
 iters = range(0, last_iteration, iteration_interval)
 m = get_metrics(qm, iters, srcdir=datadir)
 # %%
-OSEMiters = range(0, 400, 20)
+OSEMobjs = read_objectives(OSEMdir)
+OSEMiters = OSEMobjs[:, 0].astype(int)
 OSEMm = get_metrics(qm, OSEMiters, srcdir=OSEMdir)
 # %%
 fig = plt.figure()
@@ -107,7 +112,7 @@
     fig.savefig(outdir / f'{scanID}_metrics_BSREM.png')
 
 # %%
-idx = pass_index(m, numpy.array([.01, .01, .005, .005, .005]), 10)
+idx = pass_index(m, numpy.array([.01, .01] + [.005 for i in range(len(data.voi_masks))]), 10)
 iter = iters[idx]
 print(iter)
 image = STIR.ImageData(str(datadir / f"iter_{iter:04d}.hv"))

SIRF_data_preparation/run_OSEM.py

@@ -42,7 +42,7 @@
 data = get_data(srcdir=srcdir, outdir=outdir)
 # %%
 algo = main_OSEM.Submission(data, settings.num_subsets, update_objective_interval=20)
-algo.run(20, callbacks=[MetricsWithTimeout(**settings.slices, seconds=5000, outdir=outdir)])
+algo.run(400, callbacks=[MetricsWithTimeout(**settings.slices, seconds=5000, outdir=outdir)])
 # %%
 fig = plt.figure()
 data_QC.plot_image(algo.get_output(), **settings.slices)