ENH: Add schedule for the standard imaging protocol

code/sessions/hcph-sessions.py

@@ -23,9 +23,17 @@
 import datetime
 import random
 import click
+from collections import defaultdict
 import pandas as pd
 
 
+SCANNER_NAME_MAPPINGS = {
+    "Prisma": "060",
+    "Vida07": "034",
+    "VidaFit": "030",
+}
+
+
 @click.group()
 @click.version_option(message="HCPh Session Generator")
 def cli() -> None:
@@ -44,6 +52,7 @@ def cli() -> None:
 @click.option("-s", "--seed", type=click.IntRange(min=0), default=20231020)
 @click.option("-o", "--output", type=click.File("w"))
 @click.option("-n", "--num-sessions", type=click.IntRange(min=1), default=36)
+@click.option("-i", "--scanner-ids", type=str, multiple=True)
 @click.option(
     "--base-date", type=click.DateTime(formats=["%Y-%m-%d"]), default="2023-10-20"
 )
@@ -53,6 +62,7 @@ def generate(
     seed: int,
     output: click.utils.LazyFile,
     num_sessions: int,
+    scanner_ids: list[str],
     base_date: datetime.date,
     sessions_per_day: int,
     md_output: click.utils.LazyFile,
@@ -68,6 +78,8 @@ def generate(
         File to write the session plan in a tabular format.
     num_sessions : int
         Number of sessions to generate.
+    scanner_ids : list
+        Identifiers of the scanners (shuffles order).
     base_date : datetime.date
         Base date for session scheduling.
     sessions_per_day : int
@@ -84,21 +96,60 @@ def generate(
     """
 
     random.seed(seed)
+
+    num_devices = len(scanner_ids)
+
     sessions = list(range(1, num_sessions + 1))
-    encodings = (["LR", "RL", "PA", "AP"] * (num_sessions // 4 + 1))[:num_sessions]
-    random.shuffle(encodings)
     days = [
         base_date + datetime.timedelta(days=delta)
         for s in range(num_sessions)
         for delta in [s] * sessions_per_day
     ][:num_sessions]
-    table = pd.DataFrame(
-        {
-            "session": sessions,
-            "day": days,
-            "PE": encodings,
-        }
-    )
+
+    datadict = defaultdict(list)
+    for sid in scanner_ids:
+        encodings = (["LR", "RL", "PA", "AP"] * (num_sessions // 4 + 1))[:num_sessions]
+        random.shuffle(encodings)
+
+        if num_devices == 1:
+            datadict = {
+                "session": sessions,
+                "day": days,
+                "PE": encodings,
+            }
+        else:
+            datadict["day"] += days
+            datadict["device"] += [sid] * num_sessions
+            datadict["session"] += sessions
+            datadict["PE"] += encodings
+
+    table = pd.DataFrame(datadict)
+
+    if num_devices > 1:
+        indexes = list(range(len(table)))
+        random.shuffle(indexes)
+
+        table = table.iloc[indexes].sort_values(["day", "session"])
+
+        table["sessionwise_order"] = [2, 3, 4] * num_sessions
+        table.loc[table["device"] == "Prisma", "sessionwise_order"] = 1
+        table = table.sort_values(["day", "session", "sessionwise_order"])
+        table["sessionwise_order"] = [1, 2, 3] * num_sessions
+
+        table["bids_id"] = [
+            f"{row['session']:03d}{row['sessionwise_order']:02d}"
+            f"{SCANNER_NAME_MAPPINGS[row['device']]}"
+            for _, row in table.iterrows()
+        ]
+        table.reset_index(drop=True)
+        table.drop(labels=["sessionwise_order"], axis=1, inplace=True)
+
+    table["day"] = table["day"].apply(lambda x: x.date())
+
+    # print(table.to_markdown(index=False))
+    # print(table[table["device"] == "Prisma"].to_markdown(index=False))
+    # print(table[table["device"] == "Vida07"].to_markdown(index=False))
+    # print(table[table["device"] == "VidaFit"].to_markdown(index=False))
 
     if output:
         table.to_csv(output, index=None, sep="\t")

code/sessions/schedule-wave2.md

@@ -0,0 +1,38 @@
+| day        | device   |   session | PE   |   bids_id |
+|:-----------|:---------|----------:|:-----|----------:|
+| 2024-08-20 | Prisma   |         1 | AP   |  00101060 |
+| 2024-08-20 | VidaFit  |         1 | RL   |  00102030 |
+| 2024-08-20 | Vida07   |         1 | PA   |  00103034 |
+| 2024-08-21 | Prisma   |         2 | RL   |  00201060 |
+| 2024-08-21 | VidaFit  |         2 | AP   |  00202030 |
+| 2024-08-21 | Vida07   |         2 | RL   |  00203034 |
+| 2024-08-22 | Prisma   |         3 | LR   |  00301060 |
+| 2024-08-22 | Vida07   |         3 | PA   |  00302034 |
+| 2024-08-22 | VidaFit  |         3 | AP   |  00303030 |
+| 2024-08-23 | Prisma   |         4 | PA   |  00401060 |
+| 2024-08-23 | Vida07   |         4 | RL   |  00402034 |
+| 2024-08-23 | VidaFit  |         4 | RL   |  00403030 |
+| 2024-08-24 | Prisma   |         5 | RL   |  00501060 |
+| 2024-08-24 | VidaFit  |         5 | PA   |  00502030 |
+| 2024-08-24 | Vida07   |         5 | LR   |  00503034 |
+| 2024-08-25 | Prisma   |         6 | PA   |  00601060 |
+| 2024-08-25 | VidaFit  |         6 | LR   |  00602030 |
+| 2024-08-25 | Vida07   |         6 | RL   |  00603034 |
+| 2024-08-26 | Prisma   |         7 | AP   |  00701060 |
+| 2024-08-26 | VidaFit  |         7 | AP   |  00702030 |
+| 2024-08-26 | Vida07   |         7 | AP   |  00703034 |
+| 2024-08-27 | Prisma   |         8 | LR   |  00801060 |
+| 2024-08-27 | Vida07   |         8 | LR   |  00802034 |
+| 2024-08-27 | VidaFit  |         8 | PA   |  00803030 |
+| 2024-08-28 | Prisma   |         9 | PA   |  00901060 |
+| 2024-08-28 | Vida07   |         9 | AP   |  00902034 |
+| 2024-08-28 | VidaFit  |         9 | LR   |  00903030 |
+| 2024-08-29 | Prisma   |        10 | LR   |  01001060 |
+| 2024-08-29 | Vida07   |        10 | AP   |  01002034 |
+| 2024-08-29 | VidaFit  |        10 | PA   |  01003030 |
+| 2024-08-30 | Prisma   |        11 | AP   |  01101060 |
+| 2024-08-30 | VidaFit  |        11 | LR   |  01102030 |
+| 2024-08-30 | Vida07   |        11 | PA   |  01103034 |
+| 2024-08-31 | Prisma   |        12 | RL   |  01201060 |
+| 2024-08-31 | Vida07   |        12 | LR   |  01202034 |
+| 2024-08-31 | VidaFit  |        12 | RL   |  01203030 |

code/sessions/schedule-wave2.tsv

@@ -0,0 +1,37 @@
+day	device	session	PE	bids_id
+2024-08-20	Prisma	1	AP	00101060
+2024-08-20	VidaFit	1	RL	00102030
+2024-08-20	Vida07	1	PA	00103034
+2024-08-21	Prisma	2	RL	00201060
+2024-08-21	VidaFit	2	AP	00202030
+2024-08-21	Vida07	2	RL	00203034
+2024-08-22	Prisma	3	LR	00301060
+2024-08-22	Vida07	3	PA	00302034
+2024-08-22	VidaFit	3	AP	00303030
+2024-08-23	Prisma	4	PA	00401060
+2024-08-23	Vida07	4	RL	00402034
+2024-08-23	VidaFit	4	RL	00403030
+2024-08-24	Prisma	5	RL	00501060
+2024-08-24	VidaFit	5	PA	00502030
+2024-08-24	Vida07	5	LR	00503034
+2024-08-25	Prisma	6	PA	00601060
+2024-08-25	VidaFit	6	LR	00602030
+2024-08-25	Vida07	6	RL	00603034
+2024-08-26	Prisma	7	AP	00701060
+2024-08-26	VidaFit	7	AP	00702030
+2024-08-26	Vida07	7	AP	00703034
+2024-08-27	Prisma	8	LR	00801060
+2024-08-27	Vida07	8	LR	00802034
+2024-08-27	VidaFit	8	PA	00803030
+2024-08-28	Prisma	9	PA	00901060
+2024-08-28	Vida07	9	AP	00902034
+2024-08-28	VidaFit	9	LR	00903030
+2024-08-29	Prisma	10	LR	01001060
+2024-08-29	Vida07	10	AP	01002034
+2024-08-29	VidaFit	10	PA	01003030
+2024-08-30	Prisma	11	AP	01101060
+2024-08-30	VidaFit	11	LR	01102030
+2024-08-30	Vida07	11	PA	01103034
+2024-08-31	Prisma	12	RL	01201060
+2024-08-31	Vida07	12	LR	01202034
+2024-08-31	VidaFit	12	RL	01203030

docs/data-collection/participant-prep.md

@@ -14,15 +14,23 @@
         - [ ] In case of discovering any previously undisclosed contraindication, the volunteer **MUST NOT** participate in the study.
 
 - [ ] Load the adequate protocol ([guidelines here](notes-scanning.md#preparing-the-protocol)).
-    **Verify you are loading the appropriate phase-encoding (PE) direction corresponding to the session.**
+    **Verify you are loading the appropriate phase-encoding (PE) direction corresponding to the session** by checking the appropriate
+    schedule below (today is <mark>{{ now() }}</mark>).
 
-    ???+ important "Session schedule"
+    ??? important "Session schedule: *Reliability imaging protocol*"
 
-        <a name="session-schedule"></a>
-        Today is <mark>{{ now() }}</mark>:
+        <a name="session-schedule-reliability"></a>
 
 {% filter indent(width=8) %}
 {% include 'code/sessions/schedule.md' %}
+{% endfilter %}
+
+    ??? important "Session schedule: *Standard imaging protocol*"
+
+        <a name="session-schedule-standard"></a>
+
+{% filter indent(width=8) %}
+{% include 'code/sessions/schedule-wave2.md' %}
 {% endfilter %}
 
 ---

docs/data-collection/tear-up.md

@@ -285,7 +285,9 @@ A laptop should be available to fill the issue.
         ![](../assets/images/session_issue_template.png)
         - [ ] Click on <span class="consolebutton green">Get started</span> on the issue template `Scan session`.
 - [ ] Modify the title of the issue by replacing `yyy` with the session index.
-    If you don't remember the session index of today, check the [session index table](participant-prep.md#session-schedule).
+    If you don't remember the session index of today, check the session index table corresponding to the acquisition protocol:
+    [reliability imaging protocol](participant-prep.md#session-schedule-reliability),
+    or [standard imaging protocol](participant-prep.md#session-schedule-standard).
 - [ ] Verify that your phone is on ringing mode so the participants can reach you.
 - [ ] Check the time regularly to be on time to meet with the participant at the predefined location