[wip] adding afni examples

.circleci/config.yml

@@ -26,6 +26,6 @@ jobs:
           no_output_timeout: 60m
           command: |
             source ~/.bashrc
-            pytest -vs tests/test_basic_examples.py
+            pytest -vs tests
       - store_artifacts:
           path: /home/circleci/regtests

altair_plots.py

@@ -67,7 +67,8 @@ def barplot_all(self, var_l, y_scale=None, y_max_check=False, default_col="test"
         res_transf = res_plot.reset_index().melt(['env', 'index'])
         if y_scale: #should be a tuple, TODO
             if y_max_check:
-                y_max = round(self.results_flat[var_l].max().max() + .1, 2)
+                # might want to use #round(self.results_flat[var_l].max().max() + .1, 2)
+                y_max = self.results_flat[var_l].max().max() * 1.2
                 y_scale_update = (y_scale[0], y_max)
                 y_bar = alt.Y('value:Q', scale=alt.Scale(domain=y_scale_update))
             else:

cwl_generator.py

@@ -55,7 +55,9 @@ def _creating_workflow_cwl(self):
             cmd_cwl["inputs"]["input_files_{}".format(ii)]["type"] = input_tuple[0]
             cmd_cwl["inputs"]["input_files_{}".format(ii)]["inputBinding"] = {}
             cmd_cwl["inputs"]["input_files_{}".format(ii)]["inputBinding"]["position"] = ii + 2
-            cmd_cwl["inputs"]["input_files_{}".format(ii)]["inputBinding"]["prefix"] = input_tuple[1]
+            # TODO: it should be changed (using dict instead of list?)
+            if input_tuple[1]:
+                cmd_cwl["inputs"]["input_files_{}".format(ii)]["inputBinding"]["prefix"] = input_tuple[1]
 
 
         cmd_cwl["outputs"] = {}

dashboard_template/dashboard.js

@@ -101,6 +101,7 @@ d3.csv("output_all.csv", function(data) {
 	//tabulate(data, d3.keys(data[0]))
     //grid.append(tabulate(grid, data, d3.keys(data[0])));
 
+   function update(columns_new){
     // TODO: not sure if I have to update everything as in this function
     function update(columns_new){
     table.selectAll('thead').selectAll("tr").selectAll("th")
@@ -196,8 +197,6 @@ d3.csv("output_all.csv", function(data) {
         .updateAxes();
 
         update(usedaxis_list)
-
-
     });
 
         $("#selectEvents").on("select2:unselect", function(e) {
@@ -212,8 +211,7 @@ d3.csv("output_all.csv", function(data) {
         .render()
         .updateAxes();
 
-         update(usedaxis_list)
-
+        update(usedaxis_list)
     });
 });
 

testing_functions/test_afni_stat.py

@@ -0,0 +1,61 @@
+"""Comparing statistics after AFNI run (out.ss_review.FT.txt file)"""
+from __future__ import division
+import os, json, pdb
+
+
+def creating_dictionary(filename):
+    res_dict = {}
+    with open(filename) as f:
+        for line in f:
+            key_val = [k.strip() for k in line.split(":")]
+            if len(key_val) == 2:
+                try:
+                    val = [float(v) for v in key_val[1].split()]
+                except ValueError:
+                    continue
+                res_dict[key_val[0]] = val
+    return res_dict
+
+def test_file_eq(file_out, file_ref=None, name=None, **kwargs):
+    out = {}
+    dict_out = creating_dictionary(file_out)
+    dict_ref = creating_dictionary(file_ref)
+
+    for key, val_r in  dict_ref.items():
+        print("ALL KEYS: ", key, dict_ref[key], dict_out[key])
+        if (key not in dict_out.keys()) or (len(dict_out[key]) != len(dict_ref[key])):
+            error = -99999
+        else:
+            er_l = []
+            for ii in range(len(dict_ref[key])):
+                if dict_ref[key][ii] != 0:
+                    er_l.append(round(1. * abs(dict_ref[key][ii] - dict_out[key][ii]) / dict_ref[key][ii], 5))
+                elif dict_ref[key][ii] == 0 and dict_out[key][ii] != 0:
+                    er_l.append(1)
+                else:
+                    er_l.append(0)
+            error = max(er_l)
+        if ("blur" in key or "ave" in key) and ("FWHM" not in key) and ("sresp" not in key):
+            out["max_rel_error: {}".format(key)] = error
+
+    report_filename = "report_{}.json".format(name)
+    print("TEST", report_filename)
+
+
+    with open(report_filename, "w") as f:
+        json.dump(out, f)
+
+
+if __name__ == '__main__':
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    parser = ArgumentParser(description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+    parser.add_argument("-out", dest="file_out",
+                        help="file with the output for testing")
+    parser.add_argument("-ref", dest="file_ref",
+                        help="file with the reference output")
+    parser.add_argument("-name", dest="name",
+                        help="name of the test provided by a user")
+    args = parser.parse_args()
+
+    test_file_eq(**vars(args))

testrunner.py

@@ -9,4 +9,5 @@ def runner(workflow_dir):
     wf = WorkflowRegtest(workflow_dir)
     wf.run()
     wf.merging_all_output()
-    wf.dashboard_workflow()
+    wf.dashboard_workflow()
+

workflows4regtests/afni/AFNIdata6_FTanalysis_s05.ap.uber/data_input/AV1_vis.txt

@@ -0,0 +1,3 @@
+ 60 90 120 180 240
+ 120 150 180 210 270
+ 0 60 120 150 240

workflows4regtests/afni/AFNIdata6_FTanalysis_s05.ap.uber/data_input/AV2_aud.txt

@@ -0,0 +1,3 @@
+ 0 30 150 210 270
+ 0 30 60 90 240
+ 30 90 180 210 270