From 38c51506f8010e3f4af13211d831e6f5e9438a29 Mon Sep 17 00:00:00 2001 From: Andres Bercowsky Date: Fri, 30 Apr 2021 16:30:43 +0200 Subject: [PATCH 1/2] FIX: change path --- Notebooks/tractography_report.ipynb | 235 ++-------------------------- 1 file changed, 13 insertions(+), 222 deletions(-) diff --git a/Notebooks/tractography_report.ipynb b/Notebooks/tractography_report.ipynb index fb60e05..1666525 100644 --- a/Notebooks/tractography_report.ipynb +++ b/Notebooks/tractography_report.ipynb @@ -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", @@ -50,7 +41,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -60,7 +51,7 @@ " 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\")" @@ -68,7 +59,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -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", @@ -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": [ @@ -183,7 +165,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -202,7 +184,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -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' 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' 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\u001b[0m in \u001b[0;36m\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", From 19b5888e251cae82f455347697e808f62a73b7f2 Mon Sep 17 00:00:00 2001 From: Andres Bercowsky Date: Fri, 30 Apr 2021 16:37:19 +0200 Subject: [PATCH 2/2] ENH: modify gitignore --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitignore b/.gitignore index b6e4761..a4a9413 100644 --- a/.gitignore +++ b/.gitignore @@ -127,3 +127,7 @@ dmypy.json # Pyre type checker .pyre/ + +#cmp output +Notebooks/tractography_workflow/ +Notebooks/segmentation_workflow/