From 59b1b7c7294b7372e05315368049714e93200bc3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Fri, 20 Mar 2020 18:12:10 +0000
Subject: [PATCH] RF: more little tweaks
---
advanced_topics/08_fslpy.ipynb | 36 ++++++++++++++++++++++++----------
advanced_topics/08_fslpy.md | 26 +++++++++++++++---------
2 files changed, 43 insertions(+), 19 deletions(-)
diff --git a/advanced_topics/08_fslpy.ipynb b/advanced_topics/08_fslpy.ipynb
index f7d8ee0..3ca6d7d 100644
--- a/advanced_topics/08_fslpy.ipynb
+++ b/advanced_topics/08_fslpy.ipynb
@@ -1480,7 +1480,23 @@
"outputs": [],
"source": [
"jobid = run('ls', submit=True)\n",
- "print('Job ID:', jobid)\n",
+ "print('Job ID:', jobid)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Once the job finishes, we shouldd be able to read the usual `.o` and `.e`\n",
+ "files:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
"stdout = f'ls.o{jobid}'\n",
"print('Job output')\n",
"print(open(stdout).read())"
@@ -1533,9 +1549,8 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "When you submit a job, instead of passing `submit=True`, you can pass in a\n",
- "dict which contains cluster submission options - you can include any arguments\n",
- "to the\n",
+ "When you use `submit=True`, you can also specify cluster submission options -\n",
+ "you can include any arguments to the\n",
"[`fslsub.submit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html#fsl.utils.fslsub.submit)\n",
"function:"
]
@@ -1546,12 +1561,13 @@
"metadata": {},
"outputs": [],
"source": [
- "jid = runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped', submit=dict(queue='short.q'))\n",
- "jid = runfsl('bet bighead_cropped bighead_brain', submit=dict(queue='short.q', wait_for=jid))\n",
- "jid = runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=dict(queue='short.q', wait_for=jid))\n",
- "jid = runfsl('fast -o bighead_fast bighead_slices', submit=dict(queue='short.q', wait_for=jid))\n",
- "\n",
- "wait(jid)\n",
+ "jobs = []\n",
+ "jobs.append(runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped', submit=True, queue='short.q'))\n",
+ "jobs.append(runfsl('bet bighead_cropped bighead_brain', submit=True, queue='short.q', wait_for=jobs[-1]))\n",
+ "jobs.append(runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=True, queue='short.q', wait_for=jobs[-1]))\n",
+ "jobs.append(runfsl('fast -o bighead_fast bighead_slices', submit=True, queue='short.q', wait_for=jobs[-1]))\n",
+ "print('Waiting for', jobs, '...')\n",
+ "wait(jobs)\n",
"\n",
"render('-vl 80 112 91 -xh -zh -hc '\n",
" 'bighead_brain '\n",
diff --git a/advanced_topics/08_fslpy.md b/advanced_topics/08_fslpy.md
index b59a49a..21f5d74 100644
--- a/advanced_topics/08_fslpy.md
+++ b/advanced_topics/08_fslpy.md
@@ -1116,6 +1116,14 @@ ID:
```
jobid = run('ls', submit=True)
print('Job ID:', jobid)
+```
+
+
+Once the job finishes, we shouldd be able to read the usual `.o` and `.e`
+files:
+
+
+```
stdout = f'ls.o{jobid}'
print('Job output')
print(open(stdout).read())
@@ -1149,20 +1157,20 @@ render('08_fslpy/bighead bighead_brain -cm hot')
```
-When you submit a job, instead of passing `submit=True`, you can pass in a
-dict which contains cluster submission options - you can include any arguments
-to the
+When you use `submit=True`, you can also specify cluster submission options -
+you can include any arguments to the
[`fslsub.submit`](https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/fslpy/latest/fsl.utils.fslsub.html#fsl.utils.fslsub.submit)
function:
```
-jid = runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped', submit=dict(queue='short.q'))
-jid = runfsl('bet bighead_cropped bighead_brain', submit=dict(queue='short.q', wait_for=jid))
-jid = runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=dict(queue='short.q', wait_for=jid))
-jid = runfsl('fast -o bighead_fast bighead_slices', submit=dict(queue='short.q', wait_for=jid))
-
-wait(jid)
+jobs = []
+jobs.append(runfsl('robustfov -i 08_fslpy/bighead -r bighead_cropped', submit=True, queue='short.q'))
+jobs.append(runfsl('bet bighead_cropped bighead_brain', submit=True, queue='short.q', wait_for=jobs[-1]))
+jobs.append(runfsl('fslroi bighead_brain bighead_slices 0 -1 111 3 0 -1', submit=True, queue='short.q', wait_for=jobs[-1]))
+jobs.append(runfsl('fast -o bighead_fast bighead_slices', submit=True, queue='short.q', wait_for=jobs[-1]))
+print('Waiting for', jobs, '...')
+wait(jobs)
render('-vl 80 112 91 -xh -zh -hc '
'bighead_brain '
--
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