Finalizing scripts for release

Author: vfonov

README.md

@@ -36,12 +36,12 @@ Code for the paper Vladimir S. Fonov, Mahsa Dadar, The PREVENT-AD Research Group
 ## Files
 
 * Shell scripts:
-    * `download_minimal_results.sh`  - download pretrained model to run automatic qc
-    * `make_figures.sh`  - Draw Figure 2 and 3 for the paper
+    * `download_minimal_models.sh`  - download QCResNET-18 with reference pretrained model to run automatic qc (43mb)
+    * `download_all_models.sh`  - download all pretrained models to run automatic qc 
 * Directory `python`:
     * `run_all_experiments.sh` - run experiments with different versions of ResNet and SquezeNet
     * `aqc_apply.py` - apply pre-trained network
-    * `aqc_convert_to_cpu.py`- helper script to convert network from GPU to CPU 
+    * `aqc_convert_to_cpu.py`- helper script to convert network from GPU to CPU
     * `aqc_data.py` - module to load QC data
     * `aqc_training.py` - deep nearal net training script
     * `model/resnet_qc.py` - module with ResNET implementation, based on https://github.com/pytorch/vision/blob/master/torchvision/models/resnet.py
@@ -50,7 +50,7 @@ Code for the paper Vladimir S. Fonov, Mahsa Dadar, The PREVENT-AD Research Group
 * Image files:
     * `mni_icbm152_t1_tal_nlin_sym_09c_0.jpg`,`mni_icbm152_t1_tal_nlin_sym_09c_1.jpg`,`mni_icbm152_t1_tal_nlin_sym_09c_2.jpg` - reference slices, needed for both training and running pretrained model
 * `results` - figures for the paper
-* `data` - training data and reference image
+* `data` - reference images
 
 ## Validating correct operation (requires minc-toolkit and minc2_simple python module)
 

download_all_models.sh

@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e 
+prefix="https://github.com/vfonov/DARQ/releases/download/v0.1/"
+
+echo "Downloading all pretrained models"
+
+function download {
+    set -e 
+    for f in $@;do
+        if [ ! -e ${f} ];then
+        curl --location "${prefix}/${f}" -o ${f}
+        fi
+    done
+}
+
+download DARQ_models_all.tar.xz
+
+echo "Unpacking..."
+
+tar xJf DARQ_models_all.tar.xz

download_minimal_models.sh

@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e 
+prefix="https://github.com/vfonov/DARQ/releases/download/v0.1/"
+
+echo "Downloading QCResNET-18 with reference" 
+
+function download {
+    set -e 
+    for f in $@;do
+        if [ ! -e ${f} ];then
+        curl --location "${prefix}/${f}" -o ${f}
+        fi
+    done
+}
+
+download DARQ_models_minimal.tar.xz
+
+echo "Unpacking..."
+
+tar xJf DARQ_models_minimal.tar.xz

download_minimal_results_python.sh

@@ -75,10 +75,17 @@ def parse_options():
 
 
     if params.load is None:
-        params.load = default_data_dir + os.sep \
-            + ('dist' if params.dist else 'cls')+os.sep \
-            + 'model_' + params.net + ('_ref' if params.ref else '') + os.sep + \
-            'best_tnr.pth' # if params.gpu else 'best_tnr_cpu.pth' )
+
+        if params.dist:
+            params.load = default_data_dir + os.sep \
+                + 'dist' + os.sep \
+                + 'model_dist_' + params.net + ('_ref' if params.ref else '') + os.sep + \
+                'best_loss.pth' 
+        else:
+            params.load = default_data_dir + os.sep \
+                + 'cls' + os.sep \
+                + 'model_' + params.net + ('_ref' if params.ref else '') + os.sep + \
+                'best_tnr.pth'
 
     if not os.path.exists(params.load):
        print("Missing model:",params.load,file=sys.stderr)

make_figures_2_3.sh

@@ -0,0 +1,24 @@
+#! /bin/sh
+
+# figure 3: network
+dot aqc_net.dot -Tpng -Gsize=9,10\! -Gdpi=300  -o Figure_3.png
+
+# figure 2: examples
+montage -tile 4x3 \
+  -geometry +1+1 \
+    -pointsize 22 \
+  -label "" \
+  ../data/bestlinreg_claude/ADNI/002_S_0295/m72/qc/aqc_002_S_0295_m72_0.jpg \
+  ../data/bestlinreg_claude/ADNI/002_S_0295/m72/qc/aqc_002_S_0295_m72_1.jpg \
+  ../data/bestlinreg_claude/ADNI/002_S_0295/m72/qc/aqc_002_S_0295_m72_2.jpg \
+  -label "" label:"A: Passed QC" \
+  ../data/bestlinreg-xcorr/ADNI/002_S_0619/m12/qc/aqc_002_S_0619_m12_0.jpg \
+  ../data/bestlinreg-xcorr/ADNI/002_S_0619/m12/qc/aqc_002_S_0619_m12_1.jpg \
+  ../data/bestlinreg-xcorr/ADNI/002_S_0619/m12/qc/aqc_002_S_0619_m12_2.jpg \
+  -label "" label:"B: Failed QC" \
+  -label "Axial"    data/mni_icbm152_t1_tal_nlin_sym_09c_0.jpg \
+  -label "Sagittal" data/mni_icbm152_t1_tal_nlin_sym_09c_1.jpg \
+  -label "Coronal"  data/mni_icbm152_t1_tal_nlin_sym_09c_2.jpg \
+  -label "" label:"C: Reference:\nMNI ICBM 152\n2009c" \
+  Figure_2.png
+