ENH: reporting versions of software used in preproc

pypreprocess/nipype_preproc_spm_utils.py

@@ -27,9 +27,10 @@
 from subject_data import SubjectData
 from .reporting.base_reporter import (
     ResultsGallery, ProgressReport, copy_web_conf_files,
-    get_module_source_code, dict_to_html_ul)
+    get_module_source_code, dict_to_html_ul, _get_software_versions)
 from .reporting.preproc_reporter import (
-    _set_templates, generate_preproc_undergone_docstring,
+    _set_templates, generate_preproc_undergone_docstring)
+from .reporting.base_reporter import (
     get_dataset_report_log_html_template,
     get_dataset_report_preproc_html_template,
     get_dataset_report_html_template)
@@ -1659,7 +1660,8 @@ def do_subjects_preproc(subject_factory, session_ids=None, **preproc_params):
             results=parent_results_gallery, start_time=time.ctime(),
             dataset_description=dataset_description,
             source_code=user_source_code,
-            source_script_name=user_script_name)
+            source_script_name=user_script_name,
+            softwares=_get_software_versions())
         main_html = get_dataset_report_html_template(
             results=parent_results_gallery, start_time=time.ctime(),
             dataset_id=dataset_id)

pypreprocess/reporting/base_reporter.py

@@ -11,7 +11,9 @@
 import matplotlib as mpl
 import pylab as pl
 import numpy as np
+import nipype
 from ..external.tempita import HTMLTemplate, bunch
+from ..configure_spm import _configure_spm, _get_version_spm
 
 # find package path
 ROOT_DIR = os.path.split(os.path.abspath(__file__))[0]
@@ -28,6 +30,17 @@
 NIPYPE_URL = "http://nipy.sourceforge.net/nipype/"
 NISTATS_URL = "https://github.com/nistats/nistats"
 
+
+def _get_software_versions():
+    """
+    Report versions of the different software used.
+    """
+    spm_dir = _configure_spm()
+    return ["SPM: %s (found in %s)" % (_get_version_spm(spm_dir),
+                                       spm_dir),
+            "Nipype: %s" % nipype.__version__]
+
+
 def lines2breaks(lines, delimiter="\n", number_lines=False):
     """
     Converts line breaks to HTML breaks, adding `pre` tags as necessary.

pypreprocess/reporting/preproc_reporter.py

@@ -11,7 +11,6 @@
 import shutil
 import commands
 import time
-import json
 import numpy as np
 import pylab as pl
 import nibabel
@@ -25,17 +24,12 @@
 from .base_reporter import (Thumbnail,
                             ResultsGallery,
                             ProgressReport,
-                            a,
-                            img,
+                            a, img,
                             lines2breaks,
-                            get_dataset_report_html_template,
-                            get_dataset_report_preproc_html_template,
                             get_subject_report_html_template,
                             get_subject_report_preproc_html_template,
                             PYPREPROCESS_URL, DARTEL_URL, ROOT_DIR,
-                            commit_subject_thumnbail_to_parent_gallery,
-                            get_dataset_report_log_html_template,
-                            copy_web_conf_files)
+                            commit_subject_thumnbail_to_parent_gallery)
 
 
 # misc

pypreprocess/reporting/template_reports/dataset_report_preproc_template.tmpl.html

@@ -1,9 +1,9 @@
 <!-- author: d0hm4t06 3lv15 d0p91m4 -->
-
 {{default done = 0}}
 {{default preproc_undergone = None}}
 {{default dataset_description = "NOT PROVIDED!"}}
 {{default references = ["Russel A. Poldrack et al. <i>Handbook of Functional MRI Data Analysis</i>"]}}
+{{default softwares = []}}
 {{default conf_path = "."}}
 {{default source_script_name = None}}
 {{default source_code = None}}
@@ -48,15 +48,23 @@ <h2>Data pre-preprocessing</h2>
     </div>
     {{endif}}
 
-    <br/>References</b><br/>
-      <ul>
+    <br/><b>References</b><br/>
+    <ul>
       {{for ref in references}}
       <li>{{ref | html}}</li>
       {{endfor}}
-      </ul>
-      <br clear="all"/>
+    </ul>
+
+    <br/><b>Software versions</b><br/>
+    <ul>
+      {{for soft in softwares}}
+      <li>{{soft | html}}</li>
+      {{endfor}}
+    </ul>
     <hr/>
 
+    <br clear="all"/>
+
     <script type="text/javascript">
       {{py: import os; loader=os.path.basename(results.loader_filename);}}
       $('#results').load("{{loader}}").fadeIn("slow");

pypreprocess/reporting/template_reports/subject_report_preproc_template.tmpl.html

@@ -1,9 +1,9 @@
 <!-- author: d0hm4t06 3lv15 d0p91m4 -->
-
 {{default preproc_undergone = None}}
 {{default references = ["Russel A. Poldrack et al. <i>Handbook of Functional MRI Data Analysis</i>"]}}
 {{default report_html = "report.html"}}
 {{default conf_path="."}}
+{{default softwares = []}}
 
 <html>
   <head>
@@ -30,7 +30,15 @@ <h2>Data pre-preprocessing</h2>
       <li>{{ref | html}}</li>
       {{endfor}}
       </ul>
-    <hr/>
+
+      <br/><b>Software versions</b><br/>
+      <ul>
+	{{for soft in softwares}}
+	<li>{{soft | html}}</li>
+	{{endfor}}
+      </ul>
+      <hr/>
+      <hr/>
     {{endif}}
 
     <script type="text/javascript">

pypreprocess/reporting/tests/test_base_report.py

@@ -0,0 +1,10 @@
+from nose.tools import assert_true
+from pypreprocess.reporting.base_reporter import _get_software_versions
+
+
+def test_get_software_versions():
+    reports_nipype = False
+    for software in _get_software_versions():
+        if "Nipype" in software:
+            reports_nipype = True
+    assert_true(reports_nipype)

pypreprocess/subject_data.py

@@ -21,7 +21,8 @@
     commit_subject_thumnbail_to_parent_gallery,
     ResultsGallery, Thumbnail, a, img, copy_web_conf_files,
     ProgressReport, get_subject_report_html_template,
-    get_subject_report_preproc_html_template, copy_failed_png)
+    get_subject_report_preproc_html_template, copy_failed_png,
+    _get_software_versions)
 
 from .reporting.preproc_reporter import (generate_tsdiffana_thumbnail,
                                          generate_realignment_thumbnails,
@@ -588,7 +589,8 @@ def init_report(self, parent_results_gallery=None,
         # html markup
         preproc = get_subject_report_preproc_html_template(
             results=self.results_gallery, start_time=time.ctime(),
-            preproc_undergone=preproc_undergone, subject_id=self.subject_id)
+            preproc_undergone=preproc_undergone, subject_id=self.subject_id,
+            softwares=_get_software_versions())
         main_html = get_subject_report_html_template(
             start_time=time.ctime(), subject_id=self.subject_id)
         with open(self.report_preproc_filename, 'w') as fd:

pypreprocess/tests/test_subject_data.py

@@ -3,6 +3,7 @@
 from ._test_utils import _make_sd
 from pypreprocess.subject_data import SubjectData
 
+# config
 DATA_DIR = "test_tmp_data"
 if not os.path.exists(DATA_DIR):
     os.makedirs(DATA_DIR)