Add section to reports that show system info, tedana call and version

tedana/reporting/data/html/report_body_template.html

@@ -5,6 +5,13 @@
         margin-top: 50px;
         height: 900px;
     }
+    .info {
+        margin-left: 5%;
+        margin-right: 5%;
+        margin-bottom: 100px;
+        font-size: larger;
+        color: #505050;
+    }
     .about {
         position: relative;
         top: -50px;
@@ -13,11 +20,27 @@
         white-space: pre-line;
         font-family: Arial, Helvetica, sans-serif;
         font-size: larger;
+        color: #505050;
+    }
+    h1 {
+        color: #000000;
+        font-weight: 800;
+    }
+    .title {
+        color: #000000;
+        font-weight: 800;
+    }
+    td {
+        padding-right: 50px;
     }
 </style>
 <div class="content">
     $content
 </div>
+<div class="info">
+    <h1>Info</h1>
+    $info
+</div>
 <div class="about">
     $about
 </div>

tedana/reporting/data/html/report_info_table_template.html

@@ -0,0 +1,39 @@
+<div>
+    <p>
+    <span class="title">Tedana command used:</span> $command
+    </p>
+    <table>
+      <tr>
+        <td class="title">System:</td>
+        <td>$system</td>
+      </tr>
+      <tr>
+        <td class="title">Node:</td>
+        <td>$node</td>
+      </tr>
+      <tr>
+        <td class="title">Release:</td>
+        <td>$release</td>
+      </tr>
+      <tr>
+        <td class="title">System version:</td>
+        <td>$sysversion</td>
+      </tr>
+      <tr>
+        <td class="title">Machine:</td>
+        <td>$machine</td>
+      </tr>
+      <tr>
+        <td class="title">Processor:</td>
+        <td>$processor</td>
+      </tr>
+      <tr>
+        <td class="title">Python:</td>
+        <td>$python</td>
+      </tr>
+      <tr>
+        <td class="title">Tedana version:</td>
+        <td>$tedana</td>
+      </tr>
+    </table>
+  </div>

tedana/reporting/html_report.py

@@ -5,17 +5,20 @@
 from os.path import join as opj
 from string import Template
 from tedana.info import __version__
+from tedana.io import load_json
 from tedana.reporting import dynamic_figures as df
 
 
-def _update_template_bokeh(bokeh_id, about, bokeh_js):
+def _update_template_bokeh(bokeh_id, info_table, about, bokeh_js):
     """
     Populate a report with content.
 
     Parameters
     ----------
     bokeh_id : str
         HTML div created by bokeh.embed.components
+    info_table : str
+        HTML div created by _generate_info_table()
     about : str
         Reporting information for a given run
     bokeh_js : str
@@ -31,6 +34,7 @@ def _update_template_bokeh(bokeh_id, about, bokeh_js):
     with open(str(body_template_path), 'r') as body_file:
         body_tpl = Template(body_file.read())
     body = body_tpl.substitute(content=bokeh_id,
+                               info=info_table,
                                about=about,
                                javascript=bokeh_js)
     return body
@@ -55,6 +59,34 @@ def _save_as_html(body):
     return html
 
 
+def _generate_info_table(info_dict):
+    """Generate a table with relevant information about the
+    system and tedana.
+    """
+    resource_path = Path(__file__).resolve().parent.joinpath('data', 'html')
+
+    info_template_name = 'report_info_table_template.html'
+    info_template_path = resource_path.joinpath(info_template_name)
+    with open(str(info_template_path), 'r') as info_file:
+        info_tpl = Template(info_file.read())
+
+    info_dict = info_dict["GeneratedBy"][0]
+    command = info_dict["Command"]
+    version_python = info_dict["Python"]
+    info_dict = info_dict["Node"]
+
+    info_html = info_tpl.substitute(command=command,
+                                    system=info_dict["System"],
+                                    node=info_dict["Name"],
+                                    release=info_dict["Release"],
+                                    sysversion=info_dict["Version"],
+                                    machine=info_dict["Machine"],
+                                    processor=info_dict["Processor"],
+                                    python=version_python,
+                                    tedana=__version__)
+    return info_html
+
+
 def generate_report(io_generator, tr):
     """
     Parameters
@@ -114,7 +146,14 @@ def generate_report(io_generator, tr):
     with open(opj(io_generator.out_dir, 'report.txt'), 'r+') as f:
         about = f.read()
 
-    body = _update_template_bokeh(kr_div, about, kr_script)
+    # Read info table
+    data_descr_path = io_generator.get_name("data description json")
+    data_descr_dict = load_json(data_descr_path)
+
+    # Create info table
+    info_table = _generate_info_table(data_descr_dict)
+
+    body = _update_template_bokeh(kr_div, info_table, about, kr_script)
     html = _save_as_html(body)
     with open(opj(io_generator.out_dir, 'tedana_report.html'), 'wb') as f:
         f.write(html.encode('utf-8'))

tedana/utils.py

@@ -3,6 +3,7 @@
 """
 import logging
 import os.path as op
+import platform
 
 import numpy as np
 import nibabel as nib
@@ -384,3 +385,54 @@ def get_resource_path():
     Based on function by Yaroslav Halchenko used in Neurosynth Python package.
     """
     return op.abspath(op.join(op.dirname(__file__), "resources") + op.sep)
+
+
+def get_system_info():
+    """Return information about the system tedana is being run on.
+
+    Returns
+    -------
+    dict
+        Info about system where tedana is run on.
+    """
+    system_info = platform.uname()
+
+    system_dict = {
+        "System": system_info.system,
+        "Node": system_info.node,
+        "Release": system_info.release,
+        "Version": system_info.version,
+        "Machine": system_info.machine,
+        "Processor": system_info.processor,
+    }
+
+    return system_dict
+
+
+def write_tedana_command(arg_vals):
+    """Write a CLI-style command with the arguments given to run tedana.
+
+    Parameters
+    ----------
+    arg_vals : dict
+        Dictionary with arguments and values of passed to the tedana function.
+
+    Returns
+    -------
+    str
+        Arguments given to tedana and their values formatted in CLI-style.
+    """
+    # Deleta frame from dictionary
+    del arg_vals["frame"]
+
+    command = "tedana"
+
+    for key, val in arg_vals.items():
+        # Data and TE are lists
+        if type(val) is list:
+            values = " ".join(str(x) for x in val)
+        else:
+            values = val
+        command += f" <b>--{key}</b> {values}"
+
+    return command

tedana/workflows/tedana.py

@@ -1,6 +1,7 @@
 """
 Run the "canonical" TE-Dependent ANAlysis workflow.
 """
+import inspect
 import json
 import os
 import sys
@@ -340,6 +341,9 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
     generated by this workflow, please visit
     https://tedana.readthedocs.io/en/latest/outputs.html
     """
+    frame = inspect.currentframe()
+    _, _, _, arg_values = inspect.getargvalues(frame)
+
     out_dir = op.abspath(out_dir)
     if not op.isdir(out_dir):
         os.mkdir(out_dir)
@@ -421,6 +425,10 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
         verbose=verbose,
     )
 
+    # Save system info to json
+    info_dict = utils.get_system_info()
+    info_dict["Python"] = sys.version
+
     n_samp, n_echos, n_vols = catd.shape
     LGR.debug('Resulting data shape: {}'.format(catd.shape))
 
@@ -679,6 +687,9 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
     if verbose:
         io.writeresults_echoes(catd, mmix, mask, comptable, io_generator)
 
+    # Generate tedana command with all API values
+    tedana_command = utils.write_tedana_command(arg_values)
+
     # Write out BIDS-compatible description file
     derivative_metadata = {
         "Name": "tedana Outputs",
@@ -692,7 +703,17 @@ def tedana_workflow(data, tes, out_dir='.', mask=None,
                     "A denoising pipeline for the identification and removal "
                     "of non-BOLD noise from multi-echo fMRI data."
                 ),
-                "CodeURL": "https://github.com/ME-ICA/tedana"
+                "CodeURL": "https://github.com/ME-ICA/tedana",
+                "Node": {
+                    "Name": info_dict["Node"],
+                    "System": info_dict["System"],
+                    "Machine": info_dict["Machine"],
+                    "Processor": info_dict["Processor"],
+                    "Release": info_dict["Release"],
+                    "Version": info_dict["Version"]
+                },
+                "Python": info_dict["Python"],
+                "Command": tedana_command
             }
         ]
     }