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,
)