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djareckadjarecka
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changing name of graphs - removing dot
1 parent a570946 commit e8b191a

10 files changed

+503
-187
lines changed

‎notebooks/basic_graph_visualization.ipynb

Lines changed: 41 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Import the function to create an spm fmri preprocessing workflow\n",
@@ -57,7 +59,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Import relevant modules\n",
@@ -84,15 +88,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Write graph of type orig\n",
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"spmflow.write_graph(graph2use='orig', dotfilename='./graph_orig.dot')\n",
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"\n",
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"# Visualize graph\n",
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"from IPython.display import Image\n",
95-
"Image(filename=\"graph_orig.dot.png\")"
101+
"Image(filename=\"graph_orig.png\")"
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]
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},
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{
@@ -107,15 +113,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Write graph of type flat\n",
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"spmflow.write_graph(graph2use='flat', dotfilename='./graph_flat.dot')\n",
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"\n",
116124
"# Visualize graph\n",
117125
"from IPython.display import Image\n",
118-
"Image(filename=\"graph_flat.dot.png\")"
126+
"Image(filename=\"graph_flat.png\")"
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]
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},
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{
@@ -132,15 +140,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Write graph of type hierarchical\n",
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"metaflow.write_graph(graph2use='hierarchical', dotfilename='./graph_hierarchical.dot')\n",
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"\n",
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"# Visualize graph\n",
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"from IPython.display import Image\n",
143-
"Image(filename=\"graph_hierarchical.dot.png\")"
153+
"Image(filename=\"graph_hierarchical.png\")"
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]
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},
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{
@@ -155,15 +165,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Write graph of type colored\n",
162174
"metaflow.write_graph(graph2use='colored', dotfilename='./graph_colored.dot')\n",
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"\n",
164176
"# Visualize graph\n",
165177
"from IPython.display import Image\n",
166-
"Image(filename=\"graph_colored.dot.png\")"
178+
"Image(filename=\"graph_colored.png\")"
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]
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},
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{
@@ -178,15 +190,17 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Write graph of type exec\n",
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"metaflow.write_graph(graph2use='exec', dotfilename='./graph_exec.dot')\n",
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"\n",
187201
"# Visualize graph\n",
188202
"from IPython.display import Image\n",
189-
"Image(filename=\"graph_exec.dot.png\")"
203+
"Image(filename=\"graph_exec.png\")"
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]
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},
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{
@@ -205,11 +219,13 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"from IPython.display import Image\n",
212-
"Image(filename=\"graph_flat_detailed.dot.png\")"
228+
"Image(filename=\"graph_flat_detailed.png\")"
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]
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},
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{
@@ -231,11 +247,13 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"from IPython.display import Image\n",
238-
"Image(filename=\"graph_exec_detailed.dot.png\")"
256+
"Image(filename=\"graph_exec_detailed.png\")"
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]
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},
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{
@@ -259,24 +277,26 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"# Write graph of type orig\n",
266286
"spmflow.write_graph(graph2use='orig', dotfilename='./graph_orig_notSimple.dot', simple_form=False)\n",
267287
"\n",
268288
"# Visualize graph\n",
269289
"from IPython.display import Image\n",
270-
"Image(filename=\"graph_orig_notSimple.dot.png\")"
290+
"Image(filename=\"graph_orig_notSimple.png\")"
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]
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}
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],
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python [conda env:py3.5_nipype]",
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"language": "python",
279-
"name": "python3"
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"name": "conda-env-py3.5_nipype-py"
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},
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"language_info": {
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"codemirror_mode": {
@@ -288,7 +308,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.2"
311+
"version": "3.5.3"
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}
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},
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"nbformat": 4,

‎notebooks/basic_import_workflows.ipynb

Lines changed: 39 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
41+
"collapsed": true
42+
},
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"outputs": [],
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"source": [
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"from nipype.workflows.fmri.fsl.preprocess import create_susan_smooth\n",
@@ -79,7 +81,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
84+
"metadata": {
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"collapsed": true
86+
},
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"outputs": [],
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"source": [
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"!fslmaths /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz \\\n",
@@ -96,7 +100,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"smoothwf.inputs.inputnode.in_files = '/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz'\n",
@@ -115,13 +121,15 @@
115121
{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"%pylab inline\n",
122130
"from IPython.display import Image\n",
123131
"smoothwf.write_graph(graph2use='colored', format='png', simple_form=True)\n",
124-
"Image(filename='/output/susan_smooth/graph.dot.png')"
132+
"Image(filename='/output/susan_smooth/graph.png')"
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]
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},
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{
@@ -134,7 +142,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"smoothwf.run('MultiProc', plugin_args={'n_procs': 4})"
@@ -150,7 +160,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"!fslmaths /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz -Tmean fmean.nii.gz\n",
@@ -178,7 +190,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"print(smoothwf.list_node_names())"
@@ -194,7 +208,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"median = smoothwf.get_node('median')"
@@ -210,7 +226,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"median.inputs.op_string = '-k %s -p 99'"
@@ -226,7 +244,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"smoothwf.run('MultiProc', plugin_args={'n_procs': 4})"
@@ -242,7 +262,9 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": [
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"!fslmaths /output/susan_smooth/smooth/mapflow/_smooth0/sub-01_ses-test_task-fingerfootlips_bold_smooth.nii.gz \\\n",
@@ -261,21 +283,21 @@
261283
"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python [conda env:cos1]",
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"language": "python",
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"name": "python3"
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"name": "conda-env-cos1-py"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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"version": 2
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
277-
"pygments_lexer": "ipython3",
278-
"version": "3.6.2"
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"pygments_lexer": "ipython2",
300+
"version": "2.7.12"
279301
}
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},
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"nbformat": 4,

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