Quality of life improvements

gbm/jobs/cohort_submitter.sh

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

gbm/jobs/run_bip.slurm

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

gbm/jobs/run_mle.slurm

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

gbm/postprocessing/priors.ipynb

@@ -5,18 +5,7 @@
    "execution_count": null,
    "id": "a3166a39-9f5f-40d0-91f0-6d2a7270fe6c",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Warning: Process to core binding is enabled and OMP_NUM_THREADS is set to non-zero (1) value\n",
-      "If your program has OpenMP sections, this can cause over-subscription of cores and consequently poor performance\n",
-      "To avoid this, please re-run your application after setting MV2_ENABLE_AFFINITY=0\n",
-      "Use MV2_USE_THREAD_WARNING=0 to suppress this message\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
     "import sys\n",
@@ -36,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "0baeee9b-0b71-4235-9b69-17071e7595ad",
    "metadata": {},
    "outputs": [],
@@ -49,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "7aed6e35-fc35-4c4f-be85-4262675b7fc6",
    "metadata": {},
    "outputs": [],
@@ -60,7 +49,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "id": "c8143b5e-8a95-42c7-974b-69a61d2568e4",
    "metadata": {},
    "outputs": [],
@@ -79,84 +68,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "id": "0571179f-a100-46cc-b9bc-db5411c8e152",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Processing Patient: W03\n",
-      "MLE log diffusion: 0.1143035003612636\n",
-      "MLE log proliferation: -21.922898628312048\n",
-      "MLE diffusion: 1.1210923251817877\n",
-      "MLE proliferation: 3.0130483333676464e-10\n",
-      "Processing Patient: W10\n",
-      "MLE log diffusion: -1.1449908089568364\n",
-      "MLE log proliferation: -5.3926840706878\n",
-      "MLE diffusion: 0.3182268426136243\n",
-      "MLE proliferation: 0.00454974509489878\n",
-      "Processing Patient: W11\n",
-      "MLE log diffusion: -1.706727316271854\n",
-      "MLE log proliferation: -22.660688031873754\n",
-      "MLE diffusion: 0.1814586787888884\n",
-      "MLE proliferation: 1.4407486842098227e-10\n",
-      "Processing Patient: W16\n",
-      "MLE log diffusion: -0.2031689260893507\n",
-      "MLE log proliferation: -5.194750749761688\n",
-      "MLE diffusion: 0.8161403623804757\n",
-      "MLE proliferation: 0.0055455983844632465\n",
-      "Processing Patient: W18\n",
-      "MLE log diffusion: 2.061072280786489\n",
-      "MLE log proliferation: -22.081476239067886\n",
-      "MLE diffusion: 7.854387405203522\n",
-      "MLE proliferation: 2.571205077794512e-10\n",
-      "Processing Patient: W20\n",
-      "Can't process patient\n",
-      "Processing Patient: W29\n",
-      "MLE log diffusion: -1.2992952010651497\n",
-      "MLE log proliferation: -5.069853631527661\n",
-      "MLE diffusion: 0.2727239408562921\n",
-      "MLE proliferation: 0.006283339756339436\n",
-      "Processing Patient: W31\n",
-      "MLE log diffusion: 2.467532195916873\n",
-      "MLE log proliferation: -21.84418897764345\n",
-      "MLE diffusion: 11.793307339125743\n",
-      "MLE proliferation: 3.259787314492153e-10\n",
-      "Processing Patient: W35\n",
-      "MLE log diffusion: -0.7161246467064466\n",
-      "MLE log proliferation: -34.062744843271474\n",
-      "MLE diffusion: 0.4886422527555163\n",
-      "MLE proliferation: 1.6096738030043049e-15\n",
-      "Processing Patient: W36\n",
-      "MLE log diffusion: -2.1192085414669015\n",
-      "MLE log proliferation: -9.009352831042843\n",
-      "MLE diffusion: 0.12012666617230665\n",
-      "MLE proliferation: 0.00012226095391546868\n",
-      "Processing Patient: W39\n",
-      "MLE log diffusion: 233.37212716072992\n",
-      "MLE log proliferation: -13.341620428232195\n",
-      "MLE diffusion: 2.2502307540906503e+101\n",
-      "MLE proliferation: 1.6062305003569016e-06\n",
-      "Processing Patient: W43\n",
-      "MLE log diffusion: -0.5548985716113457\n",
-      "MLE log proliferation: -22.15956766981477\n",
-      "MLE diffusion: 0.5741304913739069\n",
-      "MLE proliferation: 2.3780557929506767e-10\n",
-      "Processing Patient: W50\n",
-      "MLE log diffusion: 0.2971229561335934\n",
-      "MLE log proliferation: -23.46733741675138\n",
-      "MLE diffusion: 1.3459807858674253\n",
-      "MLE proliferation: 6.430797806303075e-11\n",
-      "Processing Patient: W53\n",
-      "MLE log diffusion: 2.7033636010038573\n",
-      "MLE log proliferation: -22.495207415609546\n",
-      "MLE diffusion: 14.929865473135763\n",
-      "MLE proliferation: 1.7000259477548828e-10\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "RD_DVALUES = []\n",
     "RD_KVALUES = []\n",
@@ -203,29 +118,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "id": "bb089d1b-71ed-4290-9373-a74f7be0c61b",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Reaction diffusion WITHOUT treatment\n",
-      "Number of diffusion values: 7\n",
-      "Number of proliferation values: 3\n",
-      "Mean diffusion is: 0.3959213192772872\n",
-      "Variance of diffusion is: 0.051458666473056476\n",
-      "Mean proliferation rate is: 0.0054595610785671544\n",
-      "Variance of proliferation rate is: 5.045929506988528e-07\n",
-      "###\n",
-      "Log mean diffusion is: -1.1063448588811264\n",
-      "Log variance of diffusion is: 0.3853095522796434\n",
-      "Log mean proliferation rate is: -5.219096150659049\n",
-      "Log variance of proliferation rate is: 0.017666264680481242\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(\"Reaction diffusion WITHOUT treatment\")\n",
     "DVALUES = RD_DVALUES\n",
@@ -261,81 +157,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "id": "69a43643-a8a0-483d-b085-4c4be5da0573",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Processing Patient: W03\n",
-      "MLE log diffusion: -2.443081478669667\n",
-      "MLE log proliferation: -2.817342700006679\n",
-      "MLE diffusion: 0.08689268055104375\n",
-      "MLE proliferation: 0.05976454421266214\n",
-      "Processing Patient: W10\n",
-      "MLE log diffusion: -49.82932868352395\n",
-      "MLE log proliferation: -979.8084185123718\n",
-      "MLE diffusion: 2.287691801596685e-22\n",
-      "MLE proliferation: 0.0\n",
-      "Processing Patient: W11\n",
-      "MLE log diffusion: -3.585086338601014\n",
-      "MLE log proliferation: -3.164030796146209\n",
-      "MLE diffusion: 0.02773427298847698\n",
-      "MLE proliferation: 0.04225507575650025\n",
-      "Processing Patient: W16\n",
-      "MLE log diffusion: -3.0878809202027644\n",
-      "MLE log proliferation: -1.346505750933838\n",
-      "MLE diffusion: 0.045598478912382036\n",
-      "MLE proliferation: 0.2601476951623734\n",
-      "Processing Patient: W18\n",
-      "MLE log diffusion: -2.302602314143742\n",
-      "MLE log proliferation: -10.664932068932993\n",
-      "MLE diffusion: 0.09999827789985868\n",
-      "MLE proliferation: 2.3349568143790975e-05\n",
-      "Processing Patient: W20\n",
-      "Can't process patient\n",
-      "Processing Patient: W29\n",
-      "MLE log diffusion: -2.36765873377681\n",
-      "MLE log proliferation: -11.709701005676628\n",
-      "MLE diffusion: 0.09369984595366769\n",
-      "MLE proliferation: 8.213749778702731e-06\n",
-      "Processing Patient: W31\n",
-      "Can't process patient\n",
-      "Processing Patient: W35\n",
-      "MLE log diffusion: -21.63449432158633\n",
-      "MLE log proliferation: -2.6069018695444264\n",
-      "MLE diffusion: 4.0203003282252273e-10\n",
-      "MLE proliferation: 0.07376271664479506\n",
-      "Processing Patient: W36\n",
-      "MLE log diffusion: -2.3025850929940876\n",
-      "MLE log proliferation: -6.052240227040149\n",
-      "MLE diffusion: 0.0999999999999958\n",
-      "MLE proliferation: 0.002352585772454049\n",
-      "Processing Patient: W39\n",
-      "MLE log diffusion: -3.6039947675671646\n",
-      "MLE log proliferation: -3.0074657918687335\n",
-      "MLE diffusion: 0.027214788255300274\n",
-      "MLE proliferation: 0.04941675254814806\n",
-      "Processing Patient: W43\n",
-      "MLE log diffusion: -2.182270282641476\n",
-      "MLE log proliferation: -2.2074656620947035\n",
-      "MLE diffusion: 0.11278518551372084\n",
-      "MLE proliferation: 0.10997901962150763\n",
-      "Processing Patient: W50\n",
-      "MLE log diffusion: -3.075679974705214\n",
-      "MLE log proliferation: -2.6231396294138567\n",
-      "MLE diffusion: 0.04615823127856505\n",
-      "MLE proliferation: 0.07257464726150657\n",
-      "Processing Patient: W53\n",
-      "MLE log diffusion: -3.7115867272131595\n",
-      "MLE log proliferation: -2.901375503554706\n",
-      "MLE diffusion: 0.024438714916645614\n",
-      "MLE proliferation: 0.05494758745001253\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "RDTX_DVALUES = []\n",
     "RDTX_KVALUES = []\n",
@@ -381,29 +206,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "19f5e06c-8989-413a-a8b0-6163cc73c52e",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Reaction diffusion WITH treatment\n",
-      "Number of diffusion values: 4\n",
-      "Number of proliferation values: 6\n",
-      "Mean diffusion is: 0.06808730917391463\n",
-      "Variance of diffusion is: 0.0004990689941995712\n",
-      "Mean proliferation rate is: 0.058786887312270775\n",
-      "Variance of proliferation rate is: 0.00013186234064586555\n",
-      "###\n",
-      "Log mean diffusion is: -2.7435752768386137\n",
-      "Log variance of diffusion is: 0.11511241912075106\n",
-      "Log mean proliferation rate is: -2.853376048422435\n",
-      "Log variance of proliferation rate is: 0.03960178345019936\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "print(\"Reaction diffusion WITH treatment\")\n",
     "\n",
@@ -443,7 +249,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "id": "94db6e67-caef-48de-b456-6c39e80255cf",
    "metadata": {},
    "outputs": [],
@@ -461,19 +267,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "id": "5086802d-519e-419a-a79b-69c05e1a215f",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Physical variance of diffusion is: [0.08800584]\n",
-      "Physical variance of proliferation is: [0.03348272]\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "phys_d_var = logvar2physvar(np.mean(phys_d_vals), np.var(log_d_vals))\n",
     "phys_k_var = logvar2physvar(np.mean(phys_k_vals), np.var(log_k_vals))\n",
@@ -485,7 +282,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "gbm3.12",
    "language": "python",
    "name": "python3"
   },
@@ -499,7 +296,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,