def dr_seed_fc(): import numpy as np from os import path from labbookdb.report.tracking import treatment_group, append_external_identifiers from samri.plotting.overview import multiplot_matrix, multipage_plot from samri.utilities import bids_substitution_iterator from samri.analysis import fc db_path = '~/syncdata/meta.db' groups = treatment_group(db_path, ['cFluDW','cFluDW_'], 'cage') groups = append_external_identifiers(db_path, groups, ['Genotype_code']) all_subjects = groups['ETH/AIC'].unique() substitutions = bids_substitution_iterator( ["ofM","ofMaF","ofMcF1","ofMcF2","ofMpF"], all_subjects, ["CogB",], "~/ni_data/ofM.dr/", "composite", acquisitions=["EPI",], check_file_format='~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz') fc_results = fc.seed_based(substitutions, "~/ni_data/templates/roi/DSURQEc_dr.nii.gz", '/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii', ts_file_template='~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz', save_results="~/ni_data/ofM.dr/fc/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv_zstat.nii.gz", )
def dr_seed_fc(): import numpy as np from os import path from labbookdb.report.tracking import treatment_group, append_external_identifiers from samri.plotting.overview import multiplot_matrix, multipage_plot from samri.utilities import bids_substitution_iterator from samri.analysis import fc db_path = '~/syncdata/meta.db' groups = treatment_group(db_path, ['cFluDW','cFluDW_'], 'cage') groups = append_external_identifiers(db_path, groups, ['Genotype_code']) all_subjects = groups['ETH/AIC'].unique() substitutions = bids_substitution_iterator( ["ofM","ofMaF","ofMcF1","ofMcF2","ofMpF"], all_subjects, ["CogB",], "~/ni_data/ofM.dr/", "composite", acquisitions=["EPI",], check_file_format='~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz') fc_results = fc.seed_based(substitutions, "~/ni_data/templates/roi/DSURQEc_dr.nii.gz", "/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii", ts_file_template='~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz', save_results="~/ni_data/ofM.dr/fc/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv_zstat.nii.gz", )
def drp_seed_fc(): import numpy as np from os import path #from labbookdb.report.tracking import treatment_group, append_external_identifiers from samri.plotting.overview import multiplot_matrix, multipage_plot from samri.utilities import bids_substitution_iterator from samri.analysis import fc from samri.utilities import N_PROCS N_PROCS = max(N_PROCS - 8, 2) from bids.grabbids import BIDSLayout from bids.grabbids import BIDSValidator import os base = '~/ni_data/ofM.dr/bids/preprocessing/generic/' base = os.path.abspath(os.path.expanduser(base)) validate = BIDSValidator() for x in os.walk(base): print(x[0]) print(validate.is_bids(x[0])) layout = BIDSLayout(base) df = layout.as_data_frame() df = df[df.type.isin(['cbv'])] print(df) #substitutions = bids_substitution_iterator( # list(df['session'].unique()), # all_subjects, # ["CogB",], # "~/ni_data/ofM.dr/", # "composite", # acquisitions=["EPI",], # check_file_format='~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz') #substitutions = df.T.to_dict().values()[:2] substitutions = df.T.to_dict().values() print(substitutions) fc_results = fc.seed_based( substitutions, "~/ni_data/templates/roi/DSURQEc_drp.nii.gz", "/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii", ts_file_template= '~/ni_data/ofM.dr/bids/preprocessing/generic/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz', save_results= "~/ni_data/ofM.dr/bids/fc/DSURQEc_drp/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv_zstat.nii.gz", n_procs=N_PROCS, cachedir='/mnt/data/joblib')
def drp_seed_fc(): import numpy as np from os import path #from labbookdb.report.tracking import treatment_group, append_external_identifiers from samri.plotting.overview import multiplot_matrix, multipage_plot from samri.utilities import bids_substitution_iterator from samri.analysis import fc from samri.utilities import N_PROCS N_PROCS=max(N_PROCS-8, 2) from bids.grabbids import BIDSLayout from bids.grabbids import BIDSValidator import os base = '~/ni_data/ofM.dr/bids/preprocessing/generic/' base = os.path.abspath(os.path.expanduser(base)) validate = BIDSValidator() for x in os.walk(base): print(x[0]) print(validate.is_bids(x[0])) layout = BIDSLayout(base) df = layout.as_data_frame() df = df[df.type.isin(['cbv'])] print(df) #substitutions = bids_substitution_iterator( # list(df['session'].unique()), # all_subjects, # ["CogB",], # "~/ni_data/ofM.dr/", # "composite", # acquisitions=["EPI",], # check_file_format='~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz') #substitutions = df.T.to_dict().values()[:2] substitutions = df.T.to_dict().values() print(substitutions) fc_results = fc.seed_based(substitutions, "~/ni_data/templates/roi/DSURQEc_drp.nii.gz", "/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii", ts_file_template='~/ni_data/ofM.dr/bids/preprocessing/generic/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv.nii.gz', save_results="~/ni_data/ofM.dr/bids/fc/DSURQEc_drp/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_acq-{acquisition}_task-{task}_cbv_zstat.nii.gz", n_procs=N_PROCS, cachedir='/mnt/data/joblib')
def seed_connectivity_overview( template='/usr/share/mouse-brain-atlases/dsurqec_40micron_masked.nii', cut_coords=[None, [0, -4.9, -3.3]], plot=False, ): import numpy as np from labbookdb.report.tracking import treatment_group, append_external_identifiers from samri.plotting.overview import multiplot_matrix, multipage_plot db_path = '~/syncdata/meta.db' groups = treatment_group(db_path, ['cFluDW', 'cFluDW_'], 'cage') groups = append_external_identifiers(db_path, groups, ['Genotype_code']) all_subjects = groups['ETH/AIC'].unique() treatment = groups[(groups['Genotype_code'] == "eptg") & (groups['Cage_TreatmentProtocol_code'] == "cFluDW" )]['ETH/AIC'].tolist() no_treatment = groups[(groups['Genotype_code'] == "eptg") & (groups['Cage_TreatmentProtocol_code'] == "cFluDW_" )]['ETH/AIC'].tolist() negative_controls = groups[groups['Genotype_code'] == "epwt"]['ETH/AIC'].tolist() print(treatment, no_treatment, negative_controls) substitutions = bids_substitution_iterator( ["ofM", "ofM_aF", "ofM_cF1", "ofM_cF2", "ofM_pF"], all_subjects, [ "EPI_CBV_chr_longSOA", ], "~/ni_data/ofM.dr/", "composite", ) fc_results = fc.seed_based( substitutions, "~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz", '/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii', ts_file_template= "~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_task-{task}.nii.gz", ) print([i['subject'] for i in fc_results]) return if plot: multipage_plot( fc_results, treatment, figure_title="Chronic Fluoxetine (drinking water) Treatment Group", template=template, threshold=0.1, base_cut_coords=cut_coords, save_as="fc_treatment.pdf", overlays=['~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz'], scale=0.4, ) multipage_plot( fc_results, no_treatment, figure_title="Chronic Fluoxetine (drinking water) Treatment Group", template=template, threshold=0.1, base_cut_coords=cut_coords, save_as="fc_no_treatment.pdf", overlays=['~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz'], scale=0.4, ) multipage_plot( fc_results, negative_controls, figure_title="Chronic Fluoxetine (drinking water) Treatment Group", template=template, threshold=0.1, base_cut_coords=cut_coords, save_as="fc_negative_control.pdf", overlays=['~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz'], scale=0.4, )
def seed_connectivity_overview( template="/usr/share/mouse-brain-atlases/dsurqec_40micron_masked.nii", cut_coords=[None,[0,-4.9,-3.3]], plot=False, ): import numpy as np from labbookdb.report.tracking import treatment_group, append_external_identifiers from samri.plotting.overview import multiplot_matrix, multipage_plot db_path = '~/syncdata/meta.db' groups = treatment_group(db_path, ['cFluDW','cFluDW_'], 'cage') groups = append_external_identifiers(db_path, groups, ['Genotype_code']) all_subjects = groups['ETH/AIC'].unique() treatment = groups[ (groups['Genotype_code']=="eptg")& (groups['Cage_TreatmentProtocol_code']=="cFluDW") ]['ETH/AIC'].tolist() no_treatment = groups[ (groups['Genotype_code']=="eptg")& (groups['Cage_TreatmentProtocol_code']=="cFluDW_") ]['ETH/AIC'].tolist() negative_controls = groups[groups['Genotype_code']=="epwt"]['ETH/AIC'].tolist() print(treatment, no_treatment, negative_controls) substitutions = bids_substitution_iterator( ["ofM","ofM_aF","ofM_cF1","ofM_cF2","ofM_pF"], all_subjects, ["EPI_CBV_chr_longSOA",], "~/ni_data/ofM.dr/", "composite", ) fc_results = fc.seed_based(substitutions, "~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz", "/usr/share/mouse-brain-atlases/dsurqec_200micron_mask.nii", ts_file_template="~/ni_data/ofM.dr/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_task-{task}.nii.gz", ) print([i['subject'] for i in fc_results]) return if plot: multipage_plot(fc_results, treatment, figure_title="Chronic Fluoxetine (drinking water) Treatment Group", template=template, threshold=0.1, base_cut_coords=cut_coords, save_as="fc_treatment.pdf", overlays=['~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz'], scale=0.4, ) multipage_plot(fc_results, no_treatment, figure_title="Chronic Fluoxetine (drinking water) Treatment Group", template=template, threshold=0.1, base_cut_coords=cut_coords, save_as="fc_no_treatment.pdf", overlays=['~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz'], scale=0.4, ) multipage_plot(fc_results, negative_controls, figure_title="Chronic Fluoxetine (drinking water) Treatment Group", template=template, threshold=0.1, base_cut_coords=cut_coords, save_as="fc_negative_control.pdf", overlays=['~/ni_data/templates/roi/DSURQEc_dr_xs.nii.gz'], scale=0.4, )