Merge pull request #37 from akeshavan/wip_many

enh: a variety of new features (oops)

Author: akeshavan

Dockerfile-dmriprep

@@ -0,0 +1,6 @@
+FROM dmriprep:dev
+
+ADD . /dmriprep
+WORKDIR /dmriprep
+RUN /neurodocker/startup.sh python setup.py install
+WORKDIR /

Makefile

@@ -86,3 +86,9 @@ dist: clean ## builds source and wheel package
 
 install: clean ## install the package to the active Python's site-packages
 	python setup.py install
+
+docker-dev: ## build the development environment
+	docker build -t dmriprep:dev -f docker/Dockerfile docker/.
+
+docker: docker-dev
+	docker build -t dmriprep:prod -f Dockerfile-dmriprep .

dmriprep/cli.py

@@ -5,6 +5,7 @@
 import click
 from . import run
 from . import io
+from .data import get_dataset
 import os
 
 
@@ -50,6 +51,13 @@ def main(participant_label, bids_dir, output_dir, analysis_level="participant"):
 
     return 0
 
+@click.command()
+@click.argument('output_dir',
+                )
+def data(output_dir):
+    get_dataset(os.path.abspath(output_dir))
+    print('done')
+
 
 if __name__ == "__main__":
     sys.exit(main())  # pragma: no cover

dmriprep/qc.py

@@ -212,6 +212,7 @@ def createB0_ColorFA_Mask_Sprites(b0_file, colorFA_file, mask_file):
 
 def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
                        color_fa_file, anat_mask_file,
+                       outlier_indices,
                        outpath=op.abspath('./report.json')):
 
     report = {}
@@ -223,6 +224,7 @@ def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
     report['b0'] = b0
     report['colorFA'] = colorFA
     report['anat_mask'] = mask
+    report['outlier_volumes'] = outlier_indices.tolist()
 
     with open(eddy_report, 'r') as f:
         report['eddy_report'] = f.readlines()

dmriprep/run.py

@@ -379,6 +379,7 @@ def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
         import nibabel as nib
         import numpy as np
         import os.path as op
+        from nipype.utils.filemanip import fname_presuffix
 
         img = nib.load(op.abspath(in_file))
         img_data = img.get_fdata()
@@ -387,17 +388,17 @@ def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
 
         root, ext1 = op.splitext(in_file)
         root, ext0 = op.splitext(root)
-        out_file = ''.join([root + "_thinned", ext0, ext1])
+        out_file = fname_presuffix(in_file, suffix="_thinned", newpath=op.abspath('.')) #''.join([root + "_thinned", ext0, ext1])
         nib.save(img_thinned, op.abspath(out_file))
 
         bval = np.loadtxt(in_bval)
         bval_thinned = np.delete(bval, drop_scans, axis=0)
-        out_bval = '_thinned'.join(op.splitext(in_bval))
+        out_bval = fname_presuffix(in_bval, suffix="_thinned", newpath=op.abspath('.'))
         np.savetxt(out_bval, bval_thinned)
 
         bvec = np.loadtxt(in_bvec)
         bvec_thinned = np.delete(bvec, drop_scans, axis=1)
-        out_bvec = '_thinned'.join(op.splitext(in_bvec))
+        out_bvec = fname_presuffix(in_bvec, suffix="_thinned", newpath=op.abspath('.'))
         np.savetxt(out_bvec, bvec_thinned)
 
         return out_file, out_bval, out_bvec
@@ -546,24 +547,25 @@ def get_orig(subjects_dir, sub):
     wf.connect(convert1, "out_file", datasink, "dmriprep.anat.@anat")
 
     def reportNodeFunc(dwi_corrected_file, eddy_rms, eddy_report,
-                       color_fa_file, anat_mask_file):
+                       color_fa_file, anat_mask_file, outlier_indices):
         from dmriprep.qc import create_report_json
 
         report = create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
-                                    color_fa_file, anat_mask_file)
+                                    color_fa_file, anat_mask_file, outlier_indices)
         return report
 
     reportNode = pe.Node(niu.Function(
         input_names=['dwi_corrected_file', 'eddy_rms',
                      'eddy_report', 'color_fa_file',
-                     'anat_mask_file'],
+                     'anat_mask_file', 'outlier_indices'],
         output_names=['report'],
         function=reportNodeFunc
     ), name="reportJSON")
 
     wf.connect(prep, "outputnode.out_file", reportNode, 'dwi_corrected_file')
     wf.connect(prep, "fsl_eddy.out_movement_rms", reportNode, 'eddy_rms')
     wf.connect(prep, "fsl_eddy.out_outlier_report", reportNode, 'eddy_report')
+    wf.connect(id_outliers_node, 'drop_scans', reportNode, 'outlier_indices')
     wf.connect(threshold2, "binary_file", reportNode, 'anat_mask_file')
     wf.connect(get_tensor, "color_fa_file", reportNode, 'color_fa_file')
 
@@ -574,5 +576,5 @@ def reportNodeFunc(dwi_corrected_file, eddy_rms, eddy_report,
     wf.run()
 
     copyfile(bval_file, op.join(
-        out_dir, "dmriprep", "dwi", op.split(bval_file)[1]
+        op.abspath(out_dir), "dmriprep", "dwi", op.split(bval_file)[1]
     ))

dmriprepViewer/package-lock.json

@@ -16,6 +16,7 @@
   "dependencies": {
     "axios": "^0.18.0",
     "bootstrap-vue": "^2.0.0-rc.11",
+    "brainsprite.js": "git+https://[email protected]/SIMEXP/brainsprite.js.git",
     "d3": "^5.7.0",
     "vue": "^2.5.2",
     "vue-router": "^3.0.1",

dmriprepViewer/package.json

@@ -7,6 +7,7 @@
 <script>
 import Vue from 'vue';
 import BootstrapVue from 'bootstrap-vue';
+// eslint-disable-next-line
 import 'bootstrap/dist/css/bootstrap.css';
 import 'bootstrap-vue/dist/bootstrap-vue.css';
 

dmriprepViewer/src/App.vue

@@ -0,0 +1,71 @@
+<template>
+  <div class="brainsprite">
+        <div v-if="!done">Hold on...</div>
+        <canvas :id="id"></canvas>
+        <img :id="id+'_spriteImg'"
+         class="hidden"
+         :src="'data:image/png;base64,' + base"
+         v-if="showOrig"
+        />
+        <img :id="id+'_overlayImg'"
+         class="hidden"
+         v-if="overlay && showOrig"
+         :src="'data:image/png;base64,' + overlay"
+        />
+  </div>
+</template>
+
+<style scoped>
+  .hidden {
+    visibility: hidden;
+    /* display: none; */
+  }
+  canvas {
+    width: 100%;
+  }
+  img {
+    /* width: 10px;
+    height: 10px; */
+  }
+</style>
+
+<script>
+import brainsprite from './brainsprite';
+
+export default {
+  name: 'brainsprite',
+  props: ['base', 'overlay', 'id',
+    'base_dim_x', 'base_dim_y',
+    'overlay_dim_x', 'overlay_dim_y'],
+  data() {
+    return {
+      brain: null,
+      showOrig: true,
+      done: false,
+    };
+  },
+  methods: {
+    initBrainSprite() {
+      /* eslint-disable-next-line */
+      const brain = new brainsprite({
+        canvas: this.id,
+        sprite: `${this.id}_spriteImg`,
+        nbSlice: { Y: this.base_dim_x, Z: this.base_dim_y },
+        overlay: {
+          sprite: `${this.id}_overlayImg`,
+          nbSlice: { Y: this.overlay_dim_x, Z: this.overlay_dim_y },
+          opacity: 0.5,
+        },
+      });
+      this.brain = brain;
+      this.showOrig = false;
+      this.done = true;
+    },
+  },
+  mounted() {
+    this.$nextTick(() => {
+      setTimeout(() => { this.initBrainSprite(); }, 1);
+    });
+  },
+};
+</script>

dmriprepViewer/src/components/BrainSprite.vue

@@ -17,7 +17,7 @@
         </b-input-group-append>
       </b-input-group>
 
-      <report v-if="report.b0" :report="report"></report>
+      <report v-if="report.b0" :reportProp="report"></report>
   </b-container>
 </template>
 
@@ -27,6 +27,7 @@ import sprite4d from './Sprite4D';
 import lineChart from './LineChart';
 import report from './Report';
 
+
 export default {
   name: 'HelloWorld',
   components: {