Merge pull request #1428 from FCP-INDI/convergence/memory-estimates

⚡️ Update memory and threading estimates
FCP-INDI · Jan 30, 2021 · 827ca3e · 827ca3e
2 parents c65eeb1 + aeae2ae
commit 827ca3e
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diff --git a/CPAC/alff/alff.py b/CPAC/alff/alff.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 import os
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 from nipype.interfaces.afni import preprocess
 import nipype.interfaces.utility as util
 from CPAC.alff.utils import get_opt_string
@@ -169,7 +169,8 @@ def create_alff(wf_name='alff_workflow'):
 
     # filtering
     bandpass = pe.Node(interface=preprocess.Bandpass(),
-                       name='bandpass_filtering')
+                       name='bandpass_filtering',
+                       mem_gb=13.0)
     bandpass.inputs.outputtype = 'NIFTI_GZ'
     bandpass.inputs.out_file = os.path.join(os.path.curdir,
                                             'residual_filtered.nii.gz')

diff --git a/CPAC/anat_preproc/anat_preproc.py b/CPAC/anat_preproc/anat_preproc.py
@@ -4,7 +4,7 @@
 from nipype.interfaces import ants
 from nipype.interfaces import fsl
 from nipype.interfaces.fsl import utils as fsl_utils
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from CPAC.anat_preproc.ants import init_brain_extraction_wf
 from nipype.interfaces import freesurfer

diff --git a/CPAC/anat_preproc/ants.py b/CPAC/anat_preproc/ants.py
@@ -183,7 +183,7 @@ def init_brain_extraction_wf(tpl_target_path,
 
     copy_xform = pe.Node(CopyXForm(
         fields=['out_file', 'out_mask', 'bias_corrected', 'bias_image']),
-        name='copy_xform', run_without_submitting=True)
+        name='copy_xform', run_without_submitting=True, mem_gb=2.5)
 
     trunc = pe.MapNode(ImageMath(operation='TruncateImageIntensity', op2='0.01 0.999 256'),
                        name='truncate_images', iterfield=['op1'])
@@ -417,7 +417,7 @@ def init_atropos_wf(name='atropos_wf',
 
     copy_xform = pe.Node(CopyXForm(
         fields=['out_mask', 'out_segm', 'out_tpms']),
-        name='copy_xform', run_without_submitting=True)
+        name='copy_xform', run_without_submitting=True, mem_gb=2.5)
 
     # Run atropos (core node)
     atropos = pe.Node(Atropos(

diff --git a/CPAC/anat_preproc/lesion_preproc.py b/CPAC/anat_preproc/lesion_preproc.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 from nipype.interfaces import afni
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 
 

diff --git a/CPAC/aroma/aroma.py b/CPAC/aroma/aroma.py
@@ -1,5 +1,5 @@
 from nipype.interfaces import fsl
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from nipype.interfaces.fsl.aroma import ICA_AROMA
 

diff --git a/CPAC/aroma/aroma_test.py b/CPAC/aroma/aroma_test.py
@@ -8,7 +8,7 @@
 import os
 import glob
 import nipype.interfaces.io as nio
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 from nipype.interfaces.fsl import ImageStats
 #rom nose.tools import *
 ## This script runs the warp_nipype workflow to execute the interfaces and with the inputs already provided

diff --git a/CPAC/connectome/pipeline.py b/CPAC/connectome/pipeline.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from nipype.interfaces.base import BaseInterface, \
     BaseInterfaceInputSpec, traits, File, TraitedSpec

diff --git a/CPAC/cwas/pipeline.py b/CPAC/cwas/pipeline.py
@@ -1,6 +1,6 @@
 
 import os
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 
 from CPAC.utils.interfaces.function import Function

diff --git a/CPAC/distortion_correction/distortion_correction.py b/CPAC/distortion_correction/distortion_correction.py
@@ -5,7 +5,7 @@
 
 import nibabel as nb
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 from nipype.interfaces import afni, fsl
 import nipype.interfaces.utility as util
 import nipype.interfaces.ants as ants

diff --git a/CPAC/distortion_correction/tests/test_distortion_correction.py b/CPAC/distortion_correction/tests/test_distortion_correction.py
@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 import os
 import nipype.interfaces.io as nio
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 
 from CPAC.utils.test_resources import setup_test_wf
 from CPAC.func_preproc.func_preproc import create_func_preproc

diff --git a/CPAC/easy_thresh/easy_thresh.py b/CPAC/easy_thresh/easy_thresh.py
@@ -1,5 +1,5 @@
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.utility as util
 

diff --git a/CPAC/func_preproc/func_ingress.py b/CPAC/func_preproc/func_ingress.py
@@ -1,7 +1,7 @@
 from nipype import logging
 logger = logging.getLogger('workflow')
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 
 import nipype.interfaces.afni as afni
 

diff --git a/CPAC/func_preproc/func_preproc.py b/CPAC/func_preproc/func_preproc.py
@@ -3,7 +3,7 @@
 
 logger = logging.getLogger('workflow')
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.utility as util
 from nipype.interfaces import afni
@@ -683,7 +683,7 @@ def motion_correct_connections(wf, cfg, strat_pool, pipe_num, opt):
     elif opt == 'mcflirt':
         func_motion_correct_A = pe.Node(
             interface=fsl.MCFLIRT(save_mats=True, save_plots=True),
-            name=f'func_motion_correct_mcflirt_{pipe_num}')
+            name=f'func_motion_correct_mcflirt_{pipe_num}', mem_gb=2.5)
 
         func_motion_correct_A.inputs.save_mats = True
         func_motion_correct_A.inputs.save_plots = True
@@ -1609,15 +1609,17 @@ def func_normalize(wf, cfg, strat_pool, pipe_num, opt=None):
     '''
 
     func_normalize = pe.Node(interface=fsl.ImageMaths(),
-                             name=f'func_normalize_{pipe_num}')
+                             name=f'func_normalize_{pipe_num}',
+                             mem_gb=3.0)
     func_normalize.inputs.op_string = '-ing 10000'
     func_normalize.inputs.out_data_type = 'float'
 
     node, out = strat_pool.get_data('desc-brain_bold')
     wf.connect(node, out, func_normalize, 'in_file')
 
     func_mask_normalize = pe.Node(interface=fsl.ImageMaths(),
-                                  name=f'func_mask_normalize_{pipe_num}')
+                                  name=f'func_mask_normalize_{pipe_num}',
+                                  mem_gb=3.0)
     func_mask_normalize.inputs.op_string = '-Tmin -bin'
     func_mask_normalize.inputs.out_data_type = 'char'
 

diff --git a/CPAC/generate_motion_statistics/generate_motion_statistics.py b/CPAC/generate_motion_statistics/generate_motion_statistics.py
@@ -1,7 +1,7 @@
 import os
 import numpy as np
 import nibabel as nb
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from CPAC.utils.interfaces.function import Function
 
@@ -191,7 +191,7 @@ def motion_power_statistics(name='motion_stats',
                                  output_names=['out_file'],
                                  function=calculate_DVARS,
                                  as_module=True),
-                        name='cal_DVARS')
+                        name='cal_DVARS', mem_gb=3.5)
 
     # calculate mean DVARS
     wf.connect(input_node, 'motion_correct', cal_DVARS, 'func_brain')

diff --git a/CPAC/group_analysis/group_analysis.py b/CPAC/group_analysis/group_analysis.py
@@ -1,5 +1,5 @@
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.utility as util
 from CPAC.easy_thresh import easy_thresh

diff --git a/CPAC/image_utils/spatial_smoothing.py b/CPAC/image_utils/spatial_smoothing.py
@@ -1,6 +1,6 @@
 import nipype.interfaces.fsl as fsl
 from nipype.interfaces.afni import preprocess as afni
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from CPAC.utils import Outputs
 
@@ -51,13 +51,16 @@ def spatial_smoothing(wf_name, fwhm, input_image_type='func_derivative',
                                       ', '.join(image_types)))
 
     if opt == 'FSL':
+        output_smooth_mem_gb = 4.0
         if input_image_type == 'func_derivative_multi':
             output_smooth = pe.MapNode(interface=fsl.MultiImageMaths(),
                                        name='smooth_multi',
-                                       iterfield=['in_file'])
+                                       iterfield=['in_file'],
+                                       mem_gb=output_smooth_mem_gb)
         else:
             output_smooth = pe.Node(interface=fsl.MultiImageMaths(),
-                                    name='smooth')
+                                    name='smooth',
+                                    mem_gb=output_smooth_mem_gb)
 
     elif opt == 'AFNI':
         if input_image_type == 'func_derivative_multi':

diff --git a/CPAC/image_utils/statistical_transforms.py b/CPAC/image_utils/statistical_transforms.py
@@ -1,5 +1,5 @@
 import nipype.interfaces.fsl as fsl
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from nipype.interfaces.afni import preprocess
 from CPAC.registration import create_fsl_fnirt_nonlinear_reg, \

diff --git a/CPAC/image_utils/tests/test_smooth.py b/CPAC/image_utils/tests/test_smooth.py
@@ -1,6 +1,6 @@
 import os
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 
 from CPAC.utils.test_mocks import configuration_strategy_mock

diff --git a/CPAC/isc/pipeline.py b/CPAC/isc/pipeline.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 from nipype.interfaces.base import BaseInterface, \
     BaseInterfaceInputSpec, traits, File, TraitedSpec

diff --git a/CPAC/longitudinal_pipeline/longitudinal_preproc.py b/CPAC/longitudinal_pipeline/longitudinal_preproc.py
@@ -3,7 +3,7 @@
 import six
 import numpy as np
 import nibabel as nib
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 import nipype.interfaces.fsl as fsl
 from nipype.interfaces.fsl import ConvertXFM

diff --git a/CPAC/longitudinal_pipeline/longitudinal_workflow.py b/CPAC/longitudinal_pipeline/longitudinal_workflow.py
@@ -6,7 +6,7 @@
 
 from nipype import config
 from nipype import logging
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.afni as afni
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.io as nio

diff --git a/CPAC/median_angle/median_angle.py b/CPAC/median_angle/median_angle.py
@@ -1,4 +1,4 @@
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 
 

diff --git a/CPAC/network_centrality/network_centrality.py b/CPAC/network_centrality/network_centrality.py
@@ -36,7 +36,7 @@ def create_centrality_wf(wf_name, method_option, weight_options,
         the initialized nipype workflow for the afni centrality command
     """
 
-    import nipype.pipeline.engine as pe
+    from CPAC.pipeline import nipype_pipeline_engine as pe
     import nipype.interfaces.utility as util
     import CPAC.network_centrality.utils as utils
 

diff --git a/CPAC/network_centrality/pipeline.py b/CPAC/network_centrality/pipeline.py
@@ -1,4 +1,4 @@
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.utility as util
 
@@ -84,7 +84,8 @@ def network_centrality(wf, cfg, strat_pool, pipe_num, opt=None):
     # Resample the functional mni to the centrality mask resolution
     resample_functional_to_template = pe.Node(
         interface=fsl.FLIRT(),
-        name=f'resample_functional_to_template_{pipe_num}')
+        name=f'resample_functional_to_template_{pipe_num}',
+        mem_gb=4.0)
 
     resample_functional_to_template.inputs.set(
         interp='trilinear',

diff --git a/CPAC/nuisance/nuisance.py b/CPAC/nuisance/nuisance.py
@@ -2,7 +2,7 @@
 import os
 import numpy as np
 import nibabel as nb
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 import CPAC
 
@@ -981,7 +981,8 @@ def create_regressor_workflow(nuisance_selectors,
                     anat_resample = pe.Node(
                         interface=fsl.FLIRT(),
                         name='{}_flirt'
-                             .format(anatomical_at_resolution_key)
+                             .format(anatomical_at_resolution_key),
+                        mem_gb=8.0
                     )
                     anat_resample.inputs.apply_isoxfm = regressor_selector["extraction_resolution"]
 
@@ -1003,7 +1004,8 @@ def create_regressor_workflow(nuisance_selectors,
                     func_resample = pe.Node(
                         interface=fsl.FLIRT(),
                         name='{}_flirt'
-                             .format(functional_at_resolution_key)
+                             .format(functional_at_resolution_key),
+                        mem_gb=8.0
                     )
                     func_resample.inputs.apply_xfm = True
 
@@ -1124,7 +1126,7 @@ def create_regressor_workflow(nuisance_selectors,
                                                         'compcor_file'],
                                                     function=calc_compcor_components,
                                                     imports=compcor_imports),
-                                           name='{}_DetrendPC'.format(regressor_type), mem_gb=2.0)
+                                           name='{}_DetrendPC'.format(regressor_type), mem_gb=12.5)
 
                     compcor_node.inputs.num_components = regressor_selector['summary']['components']
 
@@ -1147,13 +1149,14 @@ def create_regressor_workflow(nuisance_selectors,
                                              'import nibabel as nb',
                                              'from nipype import logging']
 
-                        cosfilter_node = pe.Node(util.Function(input_names=['input_image_path',
-                                                                            'timestep'],
-                                                               output_names=[
-                                                                   'cosfiltered_img'],
-                                                               function=cosine_filter,
-                                                               imports=cosfilter_imports),
-                                                 name='{}_cosine_filter'.format(regressor_type))
+                        cosfilter_node = pe.Node(
+                            util.Function(input_names=['input_image_path',
+                                                       'timestep'],
+                                          output_names=['cosfiltered_img'],
+                                          function=cosine_filter,
+                                          imports=cosfilter_imports),
+                            name='{}_cosine_filter'.format(regressor_type),
+                            mem_gb=8.0)
                         nuisance_wf.connect(
                             summary_filter_input[0], summary_filter_input[1],
                             cosfilter_node, 'input_image_path'
@@ -1225,7 +1228,8 @@ def create_regressor_workflow(nuisance_selectors,
 
                         mean_node = pe.Node(
                             afni.ROIStats(quiet=False, args='-1Dformat'),
-                            name='{}_mean'.format(regressor_type)
+                            name='{}_mean'.format(regressor_type),
+                            mem_gb=5.0
                         )
                         nuisance_wf.connect(
                             summary_method_input[0], summary_method_input[1],
@@ -1561,7 +1565,7 @@ def filtering_bold_and_regressors(nuisance_selectors,
                                        'regressor_file'],
                          function=bandpass_voxels,
                          as_module=True),
-                name='frequency_filter'
+                name='frequency_filter', mem_gb=6.0
             )
 
     frequency_filter.inputs.bandpass_freqs = [

diff --git a/CPAC/nuisance/tests/test_nuisance.py b/CPAC/nuisance/tests/test_nuisance.py
@@ -1,7 +1,7 @@
 import yaml
 import glob
 
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 import nipype.interfaces.utility as util
 
 from CPAC.nuisance import create_nuisance_regression_workflow

diff --git a/CPAC/nuisance/utils/__init__.py b/CPAC/nuisance/utils/__init__.py
@@ -5,7 +5,7 @@
 import nipype.interfaces.ants as ants
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.utility as util
-import nipype.pipeline.engine as pe
+from CPAC.pipeline import nipype_pipeline_engine as pe
 from nipype.interfaces import afni
 
 from CPAC.nuisance.utils.compcor import calc_compcor_components
@@ -319,7 +319,8 @@ def generate_summarize_tissue_mask(nuisance_wf,
         elif step == 'resolution':
             mask_to_epi = pe.Node(interface=fsl.FLIRT(),
                                   name='{}_flirt'
-                                       .format(node_mask_key))
+                                       .format(node_mask_key),
+                                  mem_gb=8.0)
 
             mask_to_epi.inputs.interp = 'nearestneighbour'