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Quality of life improvements (#7)
- housekeeping - formatting - organization - support additional studies
1 parent ef5a330 commit 07dda8e

28 files changed

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‎gbm/jobs/cohort_submitter.sh‎

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@@ -17,8 +17,7 @@
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##################################################################################################
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# Define the cohort of subjects.
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# COHORT=("W03" "W10" "W11" "W16" "W18" "W20" "W29" "W31" "W35" "W36" "W39" "W43" "W50" "W53")
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COHORT=("W11" "W16" "W18" "W29" "W31" "W35" "W36" "W39" "W50" "W53")
20+
COHORT=("W03" "W11" "W16" "W29" "W35" "W36" "W43" "W53")
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# directory where patient data is stored.
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# DATADIR="${WORK}/data/IvyGAP/"
@@ -27,7 +26,7 @@ PLACEHOLDER="WXX"
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# SLURM_SCRIPT="run_VBG.slurm"
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# SLURM_SCRIPT="pp_VBG.slurm"
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# SLURM_SCRIPT="run_rd_mle.slurm"
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# SLURM_SCRIPT="run_mle.slurm"
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# SLURM_SCRIPT="run_bip.slurm"
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SLURM_SCRIPT="run_fwd_prop.slurm"
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‎gbm/jobs/run_bip.slurm‎

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@@ -56,7 +56,6 @@ NSAMPLES="500"
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PDIR="$WORK/data/IvyGAP/$SUBID/"
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BIPDIR="$SCRATCH/hgg/sub-$SUBID/${EXPNAME}_bip/"
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MESH="$SCRATCH/hgg/sub-$SUBID/bip_mesh/bip_mesh-all.h5"
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PROPDIR="$SCRATCH/hgg/sub-$SUBID/${EXPNAME}_prop/"
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# run the Bayesian inverse problem
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MV2_SMP_USE_CMA=0 ibrun apptainer run $SIF python3 -u $DT4CO_PATH/gbm/run_bip.py \

‎gbm/jobs/run_mle.slurm‎

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@@ -45,9 +45,9 @@ pwd
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SIF=$SCRATCH/containers/onco-fenics-2019.1.0_latest.sif # path to Apptainer image
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export IBRUN_TASKS_PER_NODE=56 # Set the number of tasks per node (56 is max for CLX node)
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SUBID=WXX # subject to be processed
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EXPNAME=dmrd_mle # experiment name
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EXPTYPE=rd # experiment type
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SUBID=WXX # subject to be processed
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EXPNAME=dmrdtx_mle # experiment name
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EXPTYPE=rdtx # experiment type
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# set up I/O
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PDIR=$WORK/data/IvyGAP/$SUBID/

‎gbm/postprocessing/ivygap_figs.ipynb‎

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‎gbm/postprocessing/priors.ipynb‎

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@@ -5,18 +5,7 @@
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"execution_count": null,
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"id": "a3166a39-9f5f-40d0-91f0-6d2a7270fe6c",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Warning: Process to core binding is enabled and OMP_NUM_THREADS is set to non-zero (1) value\n",
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"If your program has OpenMP sections, this can cause over-subscription of cores and consequently poor performance\n",
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"To avoid this, please re-run your application after setting MV2_ENABLE_AFFINITY=0\n",
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"Use MV2_USE_THREAD_WARNING=0 to suppress this message\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"import os\n",
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"import sys\n",
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"id": "0baeee9b-0b71-4235-9b69-17071e7595ad",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"id": "7aed6e35-fc35-4c4f-be85-4262675b7fc6",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"id": "c8143b5e-8a95-42c7-974b-69a61d2568e4",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": null,
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"id": "0571179f-a100-46cc-b9bc-db5411c8e152",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Processing Patient: W03\n",
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"MLE log diffusion: 0.1143035003612636\n",
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"MLE log proliferation: -21.922898628312048\n",
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"MLE diffusion: 1.1210923251817877\n",
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"MLE proliferation: 3.0130483333676464e-10\n",
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"Processing Patient: W10\n",
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"MLE log diffusion: -1.1449908089568364\n",
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"MLE log proliferation: -5.3926840706878\n",
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"MLE diffusion: 0.3182268426136243\n",
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"MLE proliferation: 0.00454974509489878\n",
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"Processing Patient: W11\n",
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"MLE log diffusion: -1.706727316271854\n",
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"MLE log proliferation: -22.660688031873754\n",
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"MLE diffusion: 0.1814586787888884\n",
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"MLE proliferation: 1.4407486842098227e-10\n",
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"Processing Patient: W16\n",
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"MLE log diffusion: -0.2031689260893507\n",
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"MLE log proliferation: -5.194750749761688\n",
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"MLE diffusion: 0.8161403623804757\n",
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"MLE proliferation: 0.0055455983844632465\n",
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"Processing Patient: W18\n",
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"MLE log diffusion: 2.061072280786489\n",
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"MLE log proliferation: -22.081476239067886\n",
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"MLE diffusion: 7.854387405203522\n",
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"MLE proliferation: 2.571205077794512e-10\n",
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"Processing Patient: W20\n",
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"Can't process patient\n",
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"Processing Patient: W29\n",
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"MLE log diffusion: -1.2992952010651497\n",
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"MLE log proliferation: -5.069853631527661\n",
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"MLE diffusion: 0.2727239408562921\n",
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"MLE proliferation: 0.006283339756339436\n",
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"Processing Patient: W31\n",
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"MLE log diffusion: 2.467532195916873\n",
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"MLE log proliferation: -21.84418897764345\n",
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"MLE diffusion: 11.793307339125743\n",
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"MLE proliferation: 3.259787314492153e-10\n",
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"Processing Patient: W35\n",
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"MLE log diffusion: -0.7161246467064466\n",
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"MLE log proliferation: -34.062744843271474\n",
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"MLE diffusion: 0.4886422527555163\n",
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"MLE proliferation: 1.6096738030043049e-15\n",
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"Processing Patient: W36\n",
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"MLE log diffusion: -2.1192085414669015\n",
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"MLE log proliferation: -9.009352831042843\n",
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"MLE diffusion: 0.12012666617230665\n",
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"MLE proliferation: 0.00012226095391546868\n",
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"Processing Patient: W39\n",
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"MLE log diffusion: 233.37212716072992\n",
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"MLE log proliferation: -13.341620428232195\n",
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"MLE diffusion: 2.2502307540906503e+101\n",
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"MLE proliferation: 1.6062305003569016e-06\n",
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"Processing Patient: W43\n",
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"MLE log diffusion: -0.5548985716113457\n",
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"MLE log proliferation: -22.15956766981477\n",
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"MLE diffusion: 0.5741304913739069\n",
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"MLE proliferation: 2.3780557929506767e-10\n",
147-
"Processing Patient: W50\n",
148-
"MLE log diffusion: 0.2971229561335934\n",
149-
"MLE log proliferation: -23.46733741675138\n",
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"MLE diffusion: 1.3459807858674253\n",
151-
"MLE proliferation: 6.430797806303075e-11\n",
152-
"Processing Patient: W53\n",
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"MLE log diffusion: 2.7033636010038573\n",
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"MLE log proliferation: -22.495207415609546\n",
155-
"MLE diffusion: 14.929865473135763\n",
156-
"MLE proliferation: 1.7000259477548828e-10\n"
157-
]
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}
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],
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"outputs": [],
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"source": [
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"RD_DVALUES = []\n",
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"RD_KVALUES = []\n",
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": null,
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"id": "bb089d1b-71ed-4290-9373-a74f7be0c61b",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reaction diffusion WITHOUT treatment\n",
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"Number of diffusion values: 7\n",
216-
"Number of proliferation values: 3\n",
217-
"Mean diffusion is: 0.3959213192772872\n",
218-
"Variance of diffusion is: 0.051458666473056476\n",
219-
"Mean proliferation rate is: 0.0054595610785671544\n",
220-
"Variance of proliferation rate is: 5.045929506988528e-07\n",
221-
"###\n",
222-
"Log mean diffusion is: -1.1063448588811264\n",
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"Log variance of diffusion is: 0.3853095522796434\n",
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"Log mean proliferation rate is: -5.219096150659049\n",
225-
"Log variance of proliferation rate is: 0.017666264680481242\n"
226-
]
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}
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],
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"outputs": [],
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"source": [
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"print(\"Reaction diffusion WITHOUT treatment\")\n",
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"DVALUES = RD_DVALUES\n",
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": null,
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"id": "69a43643-a8a0-483d-b085-4c4be5da0573",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Processing Patient: W03\n",
273-
"MLE log diffusion: -2.443081478669667\n",
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"MLE log proliferation: -2.817342700006679\n",
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"MLE diffusion: 0.08689268055104375\n",
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"MLE proliferation: 0.05976454421266214\n",
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"Processing Patient: W10\n",
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"MLE log diffusion: -49.82932868352395\n",
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"MLE log proliferation: -979.8084185123718\n",
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"MLE diffusion: 2.287691801596685e-22\n",
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"MLE proliferation: 0.0\n",
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"Processing Patient: W11\n",
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"MLE log diffusion: -3.585086338601014\n",
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"MLE log proliferation: -3.164030796146209\n",
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"MLE diffusion: 0.02773427298847698\n",
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"MLE proliferation: 0.04225507575650025\n",
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"Processing Patient: W16\n",
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"MLE log diffusion: -3.0878809202027644\n",
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"MLE log proliferation: -1.346505750933838\n",
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"MLE diffusion: 0.045598478912382036\n",
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"MLE proliferation: 0.2601476951623734\n",
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"Processing Patient: W18\n",
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"MLE log diffusion: -2.302602314143742\n",
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"MLE log proliferation: -10.664932068932993\n",
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"MLE diffusion: 0.09999827789985868\n",
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"MLE proliferation: 2.3349568143790975e-05\n",
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"Processing Patient: W20\n",
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"Can't process patient\n",
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"Processing Patient: W29\n",
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"MLE log diffusion: -2.36765873377681\n",
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"MLE log proliferation: -11.709701005676628\n",
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"MLE diffusion: 0.09369984595366769\n",
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"MLE proliferation: 8.213749778702731e-06\n",
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"Processing Patient: W31\n",
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"Can't process patient\n",
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"Processing Patient: W35\n",
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"MLE log diffusion: -21.63449432158633\n",
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"MLE log proliferation: -2.6069018695444264\n",
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"MLE diffusion: 4.0203003282252273e-10\n",
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"MLE proliferation: 0.07376271664479506\n",
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"Processing Patient: W36\n",
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"MLE log diffusion: -2.3025850929940876\n",
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"MLE log proliferation: -6.052240227040149\n",
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"MLE diffusion: 0.0999999999999958\n",
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"MLE proliferation: 0.002352585772454049\n",
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"Processing Patient: W39\n",
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"MLE log diffusion: -3.6039947675671646\n",
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"MLE log proliferation: -3.0074657918687335\n",
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"MLE diffusion: 0.027214788255300274\n",
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"MLE proliferation: 0.04941675254814806\n",
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"Processing Patient: W43\n",
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"MLE log diffusion: -2.182270282641476\n",
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"MLE log proliferation: -2.2074656620947035\n",
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"MLE diffusion: 0.11278518551372084\n",
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"MLE proliferation: 0.10997901962150763\n",
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"Processing Patient: W50\n",
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"MLE log diffusion: -3.075679974705214\n",
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"MLE log proliferation: -2.6231396294138567\n",
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"MLE diffusion: 0.04615823127856505\n",
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"MLE proliferation: 0.07257464726150657\n",
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"Processing Patient: W53\n",
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"MLE log diffusion: -3.7115867272131595\n",
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"MLE log proliferation: -2.901375503554706\n",
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"MLE diffusion: 0.024438714916645614\n",
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"MLE proliferation: 0.05494758745001253\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"RDTX_DVALUES = []\n",
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"RDTX_KVALUES = []\n",
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": null,
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"id": "19f5e06c-8989-413a-a8b0-6163cc73c52e",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reaction diffusion WITH treatment\n",
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"Number of diffusion values: 4\n",
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"Number of proliferation values: 6\n",
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"Mean diffusion is: 0.06808730917391463\n",
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"Variance of diffusion is: 0.0004990689941995712\n",
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"Mean proliferation rate is: 0.058786887312270775\n",
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"Variance of proliferation rate is: 0.00013186234064586555\n",
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"###\n",
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"Log mean diffusion is: -2.7435752768386137\n",
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"Log variance of diffusion is: 0.11511241912075106\n",
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"Log mean proliferation rate is: -2.853376048422435\n",
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"Log variance of proliferation rate is: 0.03960178345019936\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"print(\"Reaction diffusion WITH treatment\")\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": null,
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"id": "94db6e67-caef-48de-b456-6c39e80255cf",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "code",
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"execution_count": 15,
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"execution_count": null,
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"id": "5086802d-519e-419a-a79b-69c05e1a215f",
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Physical variance of diffusion is: [0.08800584]\n",
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"Physical variance of proliferation is: [0.03348272]\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"phys_d_var = logvar2physvar(np.mean(phys_d_vals), np.var(log_d_vals))\n",
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"phys_k_var = logvar2physvar(np.mean(phys_k_vals), np.var(log_k_vals))\n",
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485282
],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"display_name": "gbm3.12",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.9"
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"version": "3.12.4"
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}
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},
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"nbformat": 4,

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