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FIX: change path #5

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FIX: change path #5

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38c5150
FIX: change path
bercowsky Apr 30, 2021
19b5888
ENH: modify gitignore
bercowsky Apr 30, 2021
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4 changes: 4 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -127,3 +127,7 @@ dmypy.json

# Pyre type checker
.pyre/

#cmp output
Notebooks/tractography_workflow/
Notebooks/segmentation_workflow/
235 changes: 13 additions & 222 deletions Notebooks/tractography_report.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,18 +2,9 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:48:46,19 nipype.utils WARNING:\n",
"\t A newer version (1.5.1) of nipy/nipype is available. You are using 1.5.0\n"
]
}
],
"outputs": [],
"source": [
"# Imports\n",
"import os\n",
Expand Down Expand Up @@ -50,7 +41,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -60,15 +51,15 @@
" bids_ds_path = '/Volumes/SSD-Bercows/Joan/research/0_data/Sample_Multi-Modal_BIDS_dataset/ds-sample/'\n",
"\n",
"if user == 'andres':\n",
" bids_ds_path = '/home/andres/Desktop/BIDS/DS001_BIDS_andres/'\n",
" bids_ds_path = '/media/sf_UbuntuShare/BIDS/DS001_BIDS_andres/'\n",
"\n",
"deriv_cmp_dir = join(bids_ds_path, \"derivatives\", \"cmp\")\n",
"deriv_nipype_dir = join(bids_ds_path, \"nipype\", \"sub-01\", \"ses-01\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -88,9 +79,10 @@
" def _run_interface(self, runtime):\n",
"\n",
" # Call our python code here:\n",
" self.fig_file = self._tractography_plot(\n",
" self.fig_file = []\n",
" self.fig_file.append(self._tractography_plot(\n",
" self.inputs.trk_file[0]\n",
" )\n",
" ))\n",
"\n",
" # And we are done\n",
" return runtime\n",
Expand Down Expand Up @@ -130,17 +122,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"trk_path = '/home/andres/Desktop/BIDS/DS001_BIDS_andres/derivatives/cmp/sub-01/dwi/sub-01_model-CSD_desc-DET_tractogram.trk'\n",
"trk_image = dis.load_trk('/home/andres/Desktop/BIDS/DS001_BIDS_andres/derivatives/cmp/sub-01/dwi/sub-01_model-CSD_desc-DET_tractogram.trk', trk_path)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -183,7 +165,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -202,7 +184,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -214,200 +196,9 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:07,606 nipype.workflow INFO:\n",
"\t Workflow tractography_workflow settings: ['check', 'execution', 'logging', 'monitoring']\n",
"210326-16:50:07,806 nipype.workflow INFO:\n",
"\t Running serially.\n",
"210326-16:50:07,807 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"tractography_workflow.bids-grabber\" in \"/tmp/tmpxhothp5m/tractography_workflow/bids-grabber\".\n",
"210326-16:50:07,824 nipype.workflow INFO:\n",
"\t [Node] Running \"bids-grabber\" (\"nipype.interfaces.io.BIDSDataGrabber\")\n",
"210326-16:50:09,541 nipype.workflow INFO:\n",
"\t [Node] Finished \"tractography_workflow.bids-grabber\".\n",
"210326-16:50:09,542 nipype.workflow INFO:\n",
"\t [Node] Setting-up \"tractography_workflow.tractography_fig\" in \"/tmp/tmp9u6lswrj/tractography_workflow/tractography_fig\".\n",
"210326-16:50:09,546 nipype.workflow INFO:\n",
"\t [Node] Running \"tractography_fig\" (\"__main__.TractographyPlot\")\n",
"210326-16:50:17,664 nipype.workflow WARNING:\n",
"\t Storing result file without outputs\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING:nipype.workflow:Storing result file without outputs\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,665 nipype.workflow WARNING:\n",
"\t [Node] Error on \"tractography_workflow.tractography_fig\" (/tmp/tmp9u6lswrj/tractography_workflow/tractography_fig)\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING:nipype.workflow:[Node] Error on \"tractography_workflow.tractography_fig\" (/tmp/tmp9u6lswrj/tractography_workflow/tractography_fig)\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,667 nipype.workflow ERROR:\n",
"\t Node tractography_fig failed to run on host andres-VirtualBox.\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"ERROR:nipype.workflow:Node tractography_fig failed to run on host andres-VirtualBox.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,668 nipype.workflow ERROR:\n",
"\t Saving crash info to /home/andres/Desktop/BIDS/cmp3-dev/Notebooks/crash-20210326-165017-andres-tractography_fig-7a1433f2-3b42-4be1-b24d-58e288dd77a2.pklz\n",
"Traceback (most recent call last):\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py\", line 46, in run\n",
" node.run(updatehash=updatehash)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py\", line 516, in run\n",
" result = self._run_interface(execute=True)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py\", line 635, in _run_interface\n",
" return self._run_command(execute)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py\", line 741, in _run_command\n",
" result = self._interface.run(cwd=outdir)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/base/core.py\", line 399, in run\n",
" outputs = self.aggregate_outputs(runtime)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/base/core.py\", line 508, in aggregate_outputs\n",
" raise error\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/base/core.py\", line 500, in aggregate_outputs\n",
" setattr(outputs, key, val)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/trait_types.py\", line 2363, in validate\n",
" self.error(object, name, value)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/base_trait_handler.py\", line 77, in error\n",
" object, name, self.full_info(object, name, value), value\n",
"traits.trait_errors.TraitError: The 'fig_file' trait of a TractographyPlotOutputSpec instance must be a list of items which are any value, but a value of '/home/andres/Desktop/BIDS/DS001_BIDS_andres/derivatives/nipype/sub-01/tractography.png' <class 'str'> was specified.\n",
"\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"ERROR:nipype.workflow:Saving crash info to /home/andres/Desktop/BIDS/cmp3-dev/Notebooks/crash-20210326-165017-andres-tractography_fig-7a1433f2-3b42-4be1-b24d-58e288dd77a2.pklz\n",
"Traceback (most recent call last):\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py\", line 46, in run\n",
" node.run(updatehash=updatehash)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py\", line 516, in run\n",
" result = self._run_interface(execute=True)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py\", line 635, in _run_interface\n",
" return self._run_command(execute)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py\", line 741, in _run_command\n",
" result = self._interface.run(cwd=outdir)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/base/core.py\", line 399, in run\n",
" outputs = self.aggregate_outputs(runtime)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/base/core.py\", line 508, in aggregate_outputs\n",
" raise error\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/interfaces/base/core.py\", line 500, in aggregate_outputs\n",
" setattr(outputs, key, val)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/trait_types.py\", line 2363, in validate\n",
" self.error(object, name, value)\n",
" File \"/home/andres/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/traits/base_trait_handler.py\", line 77, in error\n",
" object, name, self.full_info(object, name, value), value\n",
"traits.trait_errors.TraitError: The 'fig_file' trait of a TractographyPlotOutputSpec instance must be a list of items which are any value, but a value of '/home/andres/Desktop/BIDS/DS001_BIDS_andres/derivatives/nipype/sub-01/tractography.png' <class 'str'> was specified.\n",
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,688 nipype.workflow INFO:\n",
"\t ***********************************\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"INFO:nipype.workflow:***********************************\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,689 nipype.workflow ERROR:\n",
"\t could not run node: tractography_workflow.tractography_fig\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"ERROR:nipype.workflow:could not run node: tractography_workflow.tractography_fig\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,690 nipype.workflow INFO:\n",
"\t crashfile: /home/andres/Desktop/BIDS/cmp3-dev/Notebooks/crash-20210326-165017-andres-tractography_fig-7a1433f2-3b42-4be1-b24d-58e288dd77a2.pklz\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"INFO:nipype.workflow:crashfile: /home/andres/Desktop/BIDS/cmp3-dev/Notebooks/crash-20210326-165017-andres-tractography_fig-7a1433f2-3b42-4be1-b24d-58e288dd77a2.pklz\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"210326-16:50:17,691 nipype.workflow INFO:\n",
"\t ***********************************\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"INFO:nipype.workflow:***********************************\n"
]
},
{
"ename": "RuntimeError",
"evalue": "Workflow did not execute cleanly. Check log for details",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-12-2a459d17165d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 7\u001b[0m \u001b[0mworkflow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconnect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0moverlay\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'fig_file'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreport\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'fig_file'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 9\u001b[0;31m \u001b[0mworkflow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, plugin, plugin_args, updatehash)\u001b[0m\n\u001b[1;32m 630\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mstr2bool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"execution\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"create_report\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 631\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_write_report_info\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbase_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mexecgraph\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 632\u001b[0;31m \u001b[0mrunner\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mexecgraph\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mupdatehash\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mupdatehash\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 633\u001b[0m \u001b[0mdatestr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdatetime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mutcnow\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstrftime\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"%Y%m%dT%H%M%S\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 634\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mstr2bool\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"execution\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"write_provenance\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, graph, config, updatehash)\u001b[0m\n\u001b[1;32m 68\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 69\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mold_wd\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# Return wherever we were before\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 70\u001b[0;31m \u001b[0mreport_nodes_not_run\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnotrun\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/miniconda3/envs/py37cmp-gui/lib/python3.7/site-packages/nipype/pipeline/plugins/tools.py\u001b[0m in \u001b[0;36mreport_nodes_not_run\u001b[0;34m(notrun)\u001b[0m\n\u001b[1;32m 96\u001b[0m \u001b[0mlogger\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minfo\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"***********************************\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 97\u001b[0m raise RuntimeError(\n\u001b[0;32m---> 98\u001b[0;31m \u001b[0;34m(\u001b[0m\u001b[0;34m\"Workflow did not execute cleanly. \"\u001b[0m \u001b[0;34m\"Check log for details\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 99\u001b[0m )\n\u001b[1;32m 100\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mRuntimeError\u001b[0m: Workflow did not execute cleanly. Check log for details"
]
}
],
"outputs": [],
"source": [
"workflow = Workflow(\"tractography_workflow\")\n",
"\n",
Expand Down