[ENH] generate a single report per subject for each action (#231)

* generate single report * add test * fix type * update requirements.txt * use union * rm type annotation
cpp-lln-lab · Aug 10, 2024 · 72d0e81 · 72d0e81
1 parent f04cb24
commit 72d0e81
Show file tree

Hide file tree

Showing 24 changed files with 300 additions and 81 deletions.
diff --git a/.gitignore b/.gitignore
@@ -11,7 +11,6 @@ logs
 # files
 *.nii
 *.h5
-*.html
 *desc-bidsmreye_eyetrack.tsv
 pybids_db
 tmp.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -60,7 +60,7 @@ repos:
     rev: v1.11.1
     hooks:
     -   id: mypy
-        additional_dependencies: [pydantic, numpy]
+        additional_dependencies: [pydantic, numpy, types-Jinja2]
         files: bidsmreye
         args: [--config-file, pyproject.toml]
 

diff --git a/bidsmreye/_cli.py b/bidsmreye/_cli.py
@@ -11,7 +11,7 @@
 from bidsmreye.bidsmreye import bidsmreye
 from bidsmreye.defaults import default_log_level, log_levels
 from bidsmreye.download import download
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
 
 log = bidsmreye_log(name="bidsmreye")
 

diff --git a/bidsmreye/bids_utils.py b/bidsmreye/bids_utils.py
@@ -15,7 +15,7 @@
     get_bidsname_config,
     get_pybids_config,
 )
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
 from bidsmreye.methods import methods
 from bidsmreye.utils import copy_license, create_dir_if_absent, return_regex
 

diff --git a/bidsmreye/bidsmreye.py b/bidsmreye/bidsmreye.py
@@ -9,7 +9,7 @@
 from bidsmreye._version import __version__
 from bidsmreye.configuration import Config
 from bidsmreye.defaults import default_log_level
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
 
 log = bidsmreye_log(name="bidsmreye")
 

diff --git a/bidsmreye/config/config_bidsname.json b/bidsmreye/config/config_bidsname.json
@@ -1,6 +1,6 @@
 {
     "mask": "sub-{subject}/[ses-{session}]/func/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ce}][_rec-{rec}][_dir-{dir}][_run-{run}][_space-{space}][_res-{res}][_den-{den}]_desc-eye_mask.p",
-    "report": "sub-{subject}/[ses-{session}]/func/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ce}][_rec-{rec}][_dir-{dir}][_run-{run}][_space-{space}][_res-{res}][_den-{den}]_desc-eye_report.html",
+    "report": "sub-{subject}/[ses-{session}]/figures/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ce}][_rec-{rec}][_dir-{dir}][_run-{run}][_space-{space}][_res-{res}][_den-{den}]_desc-eye_report.html",
     "no_label": "sub-{subject}/[ses-{session}]/func/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ce}][_rec-{rec}][_dir-{dir}][_run-{run}][_space-{space}][_res-{res}][_den-{den}]_desc-nolabel_bidsmreye.npz",
     "confounds_tsv": "sub-{subject}/[ses-{session}]/func/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ce}][_rec-{rec}][_dir-{dir}][_run-{run}][_space-{space}]_desc-bidsmreye_eyetrack.tsv",
     "confounds_json": "sub-{subject}/[ses-{session}]/func/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ce}][_rec-{rec}][_dir-{dir}][_run-{run}][_space-{space}]_desc-bidsmreye_eyetrack.json",

diff --git a/bidsmreye/configuration.py b/bidsmreye/configuration.py
@@ -9,7 +9,7 @@
 from attrs import asdict, converters, define, field
 from bids import BIDSLayout  # type: ignore
 
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
 
 log = bidsmreye_log(name="bidsmreye")
 

diff --git a/bidsmreye/download.py b/bidsmreye/download.py
@@ -10,7 +10,7 @@
 
 import bidsmreye
 from bidsmreye.defaults import available_models, default_model
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
 
 log = bidsmreye_log(name="bidsmreye")
 

diff --git a/bidsmreye/generalize.py b/bidsmreye/generalize.py
@@ -22,7 +22,7 @@
     list_subjects,
 )
 from bidsmreye.configuration import Config
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
 from bidsmreye.quality_control import quality_control_output
 from bidsmreye.utils import (
     add_sidecar_in_root,

diff --git a/bidsmreye/logging.py → bidsmreye/logger.py b/bidsmreye/logging.py → bidsmreye/logger.py
diff --git a/bidsmreye/methods.py b/bidsmreye/methods.py
@@ -6,10 +6,9 @@
 import warnings
 from pathlib import Path
 
-import chevron
-
 from bidsmreye._version import __version__
 from bidsmreye.defaults import available_models, default_model
+from bidsmreye.report import TEMPLATES_DIR, return_jinja_env
 from bidsmreye.utils import create_dir_for_file
 
 
@@ -44,29 +43,26 @@ def methods(
     if not model:
         model = default_model()
 
-    is_known_models = False
+    is_known_model = False
     is_default_model = False
     if model in available_models():
-        is_known_models = True
+        is_known_model = True
         if model == default_model():
             is_default_model = True
 
-    if not is_known_models:
+    if not is_known_model:
         warnings.warn(f"{model} is not a known model name.", stacklevel=3)
 
-    template_file = str(Path(__file__).parent / "templates" / "CITATION.mustache")
-    with open(template_file) as template:
-        output = chevron.render(
-            template=template,
-            data={
-                "version": __version__,
-                "model": model,
-                "is_default_model": is_default_model,
-                "is_known_models": is_known_models,
-                "qc_only": qc_only,
-            },
-            warn=True,
-        )
+    env = return_jinja_env(searchpath=TEMPLATES_DIR)
+    template = env.get_template("CITATION.jinja")
+
+    output = template.render(
+        version=__version__,
+        model=model,
+        is_default_model=is_default_model,
+        is_known_model=is_known_model,
+        qc_only=qc_only,
+    )
 
     output_file.write_text(output)
 

diff --git a/bidsmreye/prepare_data.py b/bidsmreye/prepare_data.py
@@ -20,7 +20,8 @@
     save_sampling_frequency_to_json,
 )
 from bidsmreye.configuration import Config
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
+from bidsmreye.report import generate_report
 from bidsmreye.utils import (
     check_if_file_found,
     get_deepmreye_filename,
@@ -213,4 +214,7 @@ def prepare_data(cfg: Config) -> None:
         )
         for subject_label in subjects:
             process_subject(cfg, layout_in, layout_out, subject_label)
+            generate_report(
+                output_dir=cfg.output_dir, subject_label=subject_label, action="prepare"
+            )
             progress.update(subject_loop, advance=1)
diff --git a/bidsmreye/quality_control.py b/bidsmreye/quality_control.py
@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import json
-import logging
 import math
 from pathlib import Path
 
@@ -20,7 +19,8 @@
     list_subjects,
 )
 from bidsmreye.configuration import Config
-from bidsmreye.logging import bidsmreye_log
+from bidsmreye.logger import bidsmreye_log
+from bidsmreye.report import generate_report
 from bidsmreye.utils import (
     check_if_file_found,
     create_dir_for_file,
@@ -142,9 +142,7 @@ def perform_quality_control(
     add_qc_to_sidecar(confounds, sidecar_name)
 
     fig = visualize_eye_gaze_data(confounds)
-    fig.update_layout(title=Path(confounds_tsv).name)
-    if log.isEnabledFor(logging.DEBUG):
-        fig.show()
+    fig.update_layout(showlegend=False, height=800)
 
     create_dir_for_file(visualization_html_file)
     fig.write_html(visualization_html_file)
@@ -184,6 +182,11 @@ def quality_control_output(cfg: Config) -> None:
         )
         for subject_label in subjects:
             qc_subject(cfg, layout_out, subject_label)
+            generate_report(
+                output_dir=cfg.output_dir,
+                subject_label=subject_label,
+                action="generalize",
+            )
             progress.update(subject_loop, advance=1)
 
 
@@ -203,6 +206,11 @@ def quality_control_input(cfg: Config) -> None:
         )
         for subject_label in subjects:
             qc_subject(cfg, layout_in, subject_label, layout_out)
+            generate_report(
+                output_dir=cfg.output_dir,
+                subject_label=subject_label,
+                action="generalize",
+            )
             progress.update(subject_loop, advance=1)
 
 

diff --git a/bidsmreye/report.py b/bidsmreye/report.py
@@ -0,0 +1,80 @@
+"""Compile outputs from all tasks, spaces, runs into a single HTML."""
+
+import datetime
+from pathlib import Path
+
+from jinja2 import Environment, FileSystemLoader, select_autoescape
+
+from bidsmreye._version import __version__
+from bidsmreye.logger import bidsmreye_log
+
+log = bidsmreye_log(name="bidsmreye")
+
+TEMPLATES_DIR = Path(__file__).parent / "templates"
+
+
+def return_jinja_env(searchpath=None) -> Environment:
+    if searchpath is None:
+        searchpath = TEMPLATES_DIR / "report"
+    return Environment(
+        loader=FileSystemLoader(searchpath),
+        autoescape=select_autoescape(),
+        lstrip_blocks=True,
+        trim_blocks=True,
+    )
+
+
+def generate_report(output_dir: Path, subject_label: str, action: str) -> None:
+
+    env = return_jinja_env()
+    template = env.get_template("base.html")
+
+    if action == "prepare":
+        input_files = sorted(output_dir.glob(f"sub-{subject_label}/**/*report.html"))
+    elif action == "generalize":
+        input_files = sorted(output_dir.glob(f"sub-{subject_label}/**/*eyetrack.html"))
+
+    files = []
+    for html_report in input_files:
+        with open(html_report) as f:
+            content = f.read()
+
+        name: str = html_report.stem
+        if action == "prepare":
+            name = name.replace("_desc-eye_report", "_desc-preproc_bold")
+
+        files.append({"name": name, "content": content, "path": html_report})
+
+    date = datetime.datetime.now().astimezone().replace(microsecond=0).isoformat()
+
+    report = template.render(
+        action=action,
+        files=files,
+        subject_label=subject_label,
+        date=date,
+        version=__version__,
+    )
+
+    report_filename = (
+        output_dir / f"sub-{subject_label}" / f"sub-{subject_label}_{action}.html"
+    )
+
+    with open(report_filename, "w") as f:
+        f.write(report)
+
+    log.info(f"Report saved at: '{report_filename}'.")
+
+
+if __name__ == "__main__":
+
+    cwd = Path("/home/remi/github/cpp-lln-lab/bidsMReye")
+
+    output_dir = cwd / "outputs" / "moae_fmriprep" / "derivatives" / "bidsmreye"
+    subject = "01"
+
+    output_dir = Path("/home/remi/gin/CPP/yin/bidsmreye")
+    subject_label = "02"
+
+    action = "prepare"
+
+    generate_report(output_dir, subject_label, action)
diff --git a/bidsmreye/templates/CITATION.mustache → bidsmreye/templates/CITATION.jinja b/bidsmreye/templates/CITATION.mustache → bidsmreye/templates/CITATION.jinja
@@ -6,7 +6,7 @@ performed using [*bidsMReye*](https://github.com/cpp-lln-lab/bidsMReye) (version
 a BIDS app relying on [deepMReye](https://github.com/DeepMReye/DeepMReye) (@deepmreye)
 to decode eye motion from fMRI time series data.
 
-{{^qc_only}}
+{% if not qc_only %}
 ### data extraction
 
 The data of each BOLD runs underwent co-registration conducted
@@ -28,19 +28,18 @@ across voxels (spatial normalization).
 
 Voxels time series were used as inputs for generalization decoding
 using a
-{{#is_known_models}}
+    {% if is_known_model %}
 pre-trained model {{ model }} from deepMReye from [OSF](https://osf.io/23t5v).
-    {{#is_default_model}}
+        {% if is_default_model %}
 This model was trained on the following datasets:
 guided fixations (@alexander_open_2017),
 smooth pursuit (@nau_real-motion_2018, @polti_rapid_2022, @nau_hexadirectional_2018),
 free viewing (@julian_human_2018).
-    {{/is_default_model}}
-{{/is_known_models}}
-{{^is_known_models}}
+        {% endif %}
+    {% else %}
 model trained on calibration data from the current study.
-{{/is_known_models}}
-{{/qc_only}}
+    {% endif %}
+{% endif %}
 
 ### quality control
 

diff --git a/bidsmreye/templates/report/base.html b/bidsmreye/templates/report/base.html
@@ -0,0 +1,59 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>bidsmreye report - sub-{{ subject_label }} - {{ action }}</title>
+
+    <link rel="icon" type="image/x-icon" href="https://raw.githubusercontent.com/cpp-lln-lab/bidsMReye/main/docs/source/images/bidsMReye_logo.png">
+
+    <link
+      href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-QWTKZyjpPEjISv5WaRU9OFeRpok6YctnYmDr5pNlyT2bRjXh0JMhjY6hW+ALEwIH"
+      crossorigin="anonymous"
+    />
+    <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"
+            integrity="sha384-YvpcrYf0tY3lHB60NNkmXc5s9fDVZLESaAA55NDzOxhy9GkcIdslK1eN7N6jIeHz"
+            crossorigin="anonymous">
+    </script>
+
+  </head>
+
+  <body>
+
+    <header>{% include "header.html" %}</header>
+
+    <main class="container-fluid">
+
+      <h2 class="mt-5 pt-5">subject {{ subject_label }}: {{ action }}</h2>
+
+      {% for file in files %}
+      <section id="{{ file.name }}">
+        <div class="row pt-4 px-5">
+          <h3 class="pt-3">{{ file.name }}</h3>
+          <div class="rounded-2 {% if action == 'prepare' %} bg-black {% else %} bg-white {% endif %}">
+            <div class="m-2 p-2">{{ file.content|safe }}</div>
+          </div>
+        </div>
+      </section>
+      {% endfor %}
+
+      <section id="about">
+        <h2 class="mt-3">About</h2>
+        <p>
+          Report generated
+          <ul>
+            <li>on: {{ date }}</li>
+            <li>with bidsmreye {{ version }}</li>
+          </ul>
+        </p>
+      </section>
+
+    </main>
+
+    <footer>{% include "footer.html" %}</footer>
+
+  </body>
+</html>