@pencil-agent/nano-pencil 2.0.0 → 2.0.1

package/dist/extensions/builtin/browser/agent-workspace/domain-skills/centilebrain/generate-estimates.md

@@ -1,110 +1,110 @@
-# CentileBrain — Generate Normative Deviation Values
-
-URL: `https://centilebrain.org/#/model`
-
-Generates z-scores for a single subject's FreeSurfer-derived morphometry
-against the CentileBrain normative reference. Three separate modalities
-(`SubcorticalVolume`, `CorticalThickness`, `SurfaceArea`), two sexes,
-each a distinct Shiny app. Login/account not required.
-
-## Site shape
-
-- The `/#/model` page is a thin wrapper around per-modality/sex **Shiny
-  iframes** at `https://centilebrain-app.shinyapps.io/{SV|CT|SA}-{MALE|FEMALE}/`.
-- Switching modality swaps the iframe; switching sex swaps the iframe.
-  The top-page buttons and toggles are not forms — they just replace
-  the iframe `src`.
-- The upload form, compute button, and download link all live **inside the iframe**.
-  `iframe_target("shinyapps.io/SV-MALE")` (etc.) returns the session to use.
-- Requires `upload_file(..., target_id=...)` — the iframe-aware upload helper.
-
-## Form elements (inside the iframe)
-
-| Selector | Purpose |
-|---|---|
-| `#email` | Required text input. Any valid-looking string works; it does not send mail. |
-| `#file1` | The file input. Accepts the official `.xlsx` template for that modality/sex (download from the site to see the expected schema). |
-| `#confirm` | The **Compute** button. Click exactly once after upload. |
-| `#downloadData1` | **Download Results** link once compute is done. Produces a zip of CSVs + xlsx. |
-
-## Waits
-
-- Upload: after `upload_file`, wait ~3 s for the Shiny server to read the file; the data preview table populates in-place.
-- Compute: poll the iframe body text for `"Computation complete"` — typically 30-90 s. `"Computing… This may take a few seconds to a couple of minutes."` is the in-progress marker.
-- Download: click `#downloadData1`, then poll the Chrome download directory for a `{SV|CT|SA}_{male|female}_YYYY-MM-DD-HH-MM-SS.zip`. Set `Browser.setDownloadBehavior` with a known `downloadPath` before clicking so you can find it deterministically.
-
-## Traps
-
-- **Iframe target_id goes stale across modality swaps.** After clicking `CORTICAL THICKNESS` or `SURFACE AREA`, re-call `iframe_target("shinyapps.io/CT-MALE")` — the old id from SV-MALE will not work even though `Target.getTargets` may still list it briefly. Add a 2-3 s sleep after the modality-swap click before re-resolving.
-- **Sex toggles are MUI switches, not radio buttons.** They are `input[type=checkbox]` with `name=female` / `name=male`. Clicking one does not automatically uncheck the other visibly, but the iframe src changes based on which is `checked`. Easiest: `js("document.querySelector('input[name=male]').click()")`.
-- **Top-level buttons scroll off-screen after first interaction.** The modality buttons are at `y ≈ 226`, but after scrolling/iframe expansion they report `y < 0`. Use `js("window.scrollTo(0, 0)")` then click via JS by text (`Array.from(document.querySelectorAll('button')).find(b => b.innerText.trim() === 'CORTICAL THICKNESS').click()`) instead of fixed coordinates.
-
-## End-to-end example
-
-```python
-import time, os
-
-DL = "/tmp/centilebrain"
-os.makedirs(DL, exist_ok=True)
-cdp("Browser.setDownloadBehavior", behavior="allow", downloadPath=DL, eventsEnabled=True)
-
-new_tab("https://centilebrain.org/#/model")
-wait_for_load()
-time.sleep(2)
-
-# Pick modality + sex (SV + male shown; repeat for CT and SA as needed)
-js("""Array.from(document.querySelectorAll('button'))
-       .find(b => b.innerText.trim() === 'SUBCORTICAL VOLUME').click()""")
-time.sleep(1)
-js("document.querySelector('input[name=male]').click()")
-time.sleep(2)
-
-t = iframe_target("shinyapps.io/SV-MALE")
-upload_file("#file1", "/abs/path/JMT_subcortical_volume.xlsx", target_id=t)
-time.sleep(3)
-
-js("""const e=document.querySelector('#email');
-      e.value='user@example.com';
-      e.dispatchEvent(new Event('input',{bubbles:true}));""", target_id=t)
-
-js("document.querySelector('#confirm').click()", target_id=t)
-for _ in range(40):
-    time.sleep(3)
-    if "Computation complete" in js("document.body.innerText", target_id=t):
-        break
-
-before = set(os.listdir(DL))
-js("document.querySelector('#downloadData1').click()", target_id=t)
-for _ in range(30):
-    time.sleep(2)
-    after = set(os.listdir(DL))
-    new = after - before
-    if new and not any(f.endswith(".crdownload") for f in after):
-        print("downloaded:", new)
-        break
-```
-
-## Output zip
-
-Unzipped contents (SV example):
-
-```
-output_file_YYYY-MM-DD-HH-MM-SS/
-  zscore_SubcorticalVolume_male.csv       # per-ROI z-scores
-  prediction_SubcorticalVolume_male.csv   # model-predicted raw values
-  centile_SubcorticalVolume_male.xlsx     # centile ranks
-  MAE_SubcorticalVolume_male.csv          # model accuracy (not per-subject)
-  RMSE_SubcorticalVolume_male.csv
-  Corr_SubcorticalVolume_male.csv
-  EV_SubcorticalVolume_male.csv
-```
-
-The `zscore_*.csv` is the file you almost always want. Columns are
-`SITE, SubjectID, Vendor, FreeSurfer_Version, age, <ROIs...>`.
-
-## Multi-subject / batch uploads
-
-The `.xlsx` template accepts many rows, and CentileBrain processes them
-all in one compute. Same flow, same iframe; the z-score CSV will have
-one row per subject. No concurrency needed across modality/sex for a
-typical cohort.
+# CentileBrain — Generate Normative Deviation Values
+
+URL: `https://centilebrain.org/#/model`
+
+Generates z-scores for a single subject's FreeSurfer-derived morphometry
+against the CentileBrain normative reference. Three separate modalities
+(`SubcorticalVolume`, `CorticalThickness`, `SurfaceArea`), two sexes,
+each a distinct Shiny app. Login/account not required.
+
+## Site shape
+
+- The `/#/model` page is a thin wrapper around per-modality/sex **Shiny
+  iframes** at `https://centilebrain-app.shinyapps.io/{SV|CT|SA}-{MALE|FEMALE}/`.
+- Switching modality swaps the iframe; switching sex swaps the iframe.
+  The top-page buttons and toggles are not forms — they just replace
+  the iframe `src`.
+- The upload form, compute button, and download link all live **inside the iframe**.
+  `iframe_target("shinyapps.io/SV-MALE")` (etc.) returns the session to use.
+- Requires `upload_file(..., target_id=...)` — the iframe-aware upload helper.
+
+## Form elements (inside the iframe)
+
+| Selector | Purpose |
+|---|---|
+| `#email` | Required text input. Any valid-looking string works; it does not send mail. |
+| `#file1` | The file input. Accepts the official `.xlsx` template for that modality/sex (download from the site to see the expected schema). |
+| `#confirm` | The **Compute** button. Click exactly once after upload. |
+| `#downloadData1` | **Download Results** link once compute is done. Produces a zip of CSVs + xlsx. |
+
+## Waits
+
+- Upload: after `upload_file`, wait ~3 s for the Shiny server to read the file; the data preview table populates in-place.
+- Compute: poll the iframe body text for `"Computation complete"` — typically 30-90 s. `"Computing… This may take a few seconds to a couple of minutes."` is the in-progress marker.
+- Download: click `#downloadData1`, then poll the Chrome download directory for a `{SV|CT|SA}_{male|female}_YYYY-MM-DD-HH-MM-SS.zip`. Set `Browser.setDownloadBehavior` with a known `downloadPath` before clicking so you can find it deterministically.
+
+## Traps
+
+- **Iframe target_id goes stale across modality swaps.** After clicking `CORTICAL THICKNESS` or `SURFACE AREA`, re-call `iframe_target("shinyapps.io/CT-MALE")` — the old id from SV-MALE will not work even though `Target.getTargets` may still list it briefly. Add a 2-3 s sleep after the modality-swap click before re-resolving.
+- **Sex toggles are MUI switches, not radio buttons.** They are `input[type=checkbox]` with `name=female` / `name=male`. Clicking one does not automatically uncheck the other visibly, but the iframe src changes based on which is `checked`. Easiest: `js("document.querySelector('input[name=male]').click()")`.
+- **Top-level buttons scroll off-screen after first interaction.** The modality buttons are at `y ≈ 226`, but after scrolling/iframe expansion they report `y < 0`. Use `js("window.scrollTo(0, 0)")` then click via JS by text (`Array.from(document.querySelectorAll('button')).find(b => b.innerText.trim() === 'CORTICAL THICKNESS').click()`) instead of fixed coordinates.
+
+## End-to-end example
+
+```python
+import time, os
+
+DL = "/tmp/centilebrain"
+os.makedirs(DL, exist_ok=True)
+cdp("Browser.setDownloadBehavior", behavior="allow", downloadPath=DL, eventsEnabled=True)
+
+new_tab("https://centilebrain.org/#/model")
+wait_for_load()
+time.sleep(2)
+
+# Pick modality + sex (SV + male shown; repeat for CT and SA as needed)
+js("""Array.from(document.querySelectorAll('button'))
+       .find(b => b.innerText.trim() === 'SUBCORTICAL VOLUME').click()""")
+time.sleep(1)
+js("document.querySelector('input[name=male]').click()")
+time.sleep(2)
+
+t = iframe_target("shinyapps.io/SV-MALE")
+upload_file("#file1", "/abs/path/JMT_subcortical_volume.xlsx", target_id=t)
+time.sleep(3)
+
+js("""const e=document.querySelector('#email');
+      e.value='user@example.com';
+      e.dispatchEvent(new Event('input',{bubbles:true}));""", target_id=t)
+
+js("document.querySelector('#confirm').click()", target_id=t)
+for _ in range(40):
+    time.sleep(3)
+    if "Computation complete" in js("document.body.innerText", target_id=t):
+        break
+
+before = set(os.listdir(DL))
+js("document.querySelector('#downloadData1').click()", target_id=t)
+for _ in range(30):
+    time.sleep(2)
+    after = set(os.listdir(DL))
+    new = after - before
+    if new and not any(f.endswith(".crdownload") for f in after):
+        print("downloaded:", new)
+        break
+```
+
+## Output zip
+
+Unzipped contents (SV example):
+
+```
+output_file_YYYY-MM-DD-HH-MM-SS/
+  zscore_SubcorticalVolume_male.csv       # per-ROI z-scores
+  prediction_SubcorticalVolume_male.csv   # model-predicted raw values
+  centile_SubcorticalVolume_male.xlsx     # centile ranks
+  MAE_SubcorticalVolume_male.csv          # model accuracy (not per-subject)
+  RMSE_SubcorticalVolume_male.csv
+  Corr_SubcorticalVolume_male.csv
+  EV_SubcorticalVolume_male.csv
+```
+
+The `zscore_*.csv` is the file you almost always want. Columns are
+`SITE, SubjectID, Vendor, FreeSurfer_Version, age, <ROIs...>`.
+
+## Multi-subject / batch uploads
+
+The `.xlsx` template accepts many rows, and CentileBrain processes them
+all in one compute. Same flow, same iframe; the z-score CSV will have
+one row per subject. No concurrency needed across modality/sex for a
+typical cohort.