def build_input_node(self):
"""Build and connect an input node to the pipeline."""
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
from clinica.utils.exceptions import ClinicaException, ClinicaCAPSError
from clinica.utils.inputs import clinica_file_reader, clinica_group_reader
from clinica.utils.input_files import t1_volume_i_th_iteration_group_template, t1_volume_dartel_input_tissue
from clinica.utils.ux import print_images_to_process
read_input_node = npe.Node(name="LoadingCLIArguments",
interface=nutil.IdentityInterface(
fields=self.get_input_fields(),
mandatory_inputs=True))
all_errors = []
# Dartel Input Tissues
# ====================
d_input = []
for tissue_number in self.parameters['tissues']:
try:
current_file = clinica_file_reader(
self.subjects, self.sessions, self.caps_directory,
t1_volume_dartel_input_tissue(tissue_number))
d_input.append(current_file)
except ClinicaException as e:
all_errors.append(e)
# Dartel Templates
# ================
dartel_iter_templates = []
for i in range(1, 7):
try:
current_iter = clinica_group_reader(
self.caps_directory,
t1_volume_i_th_iteration_group_template(
self.parameters['group_id'], i))
dartel_iter_templates.append(current_iter)
except ClinicaException as e:
all_errors.append(e)
if len(all_errors) > 0:
error_message = 'Clinica faced error(s) while trying to read files in your CAPS/BIDS directories.\n'
for msg in all_errors:
error_message += str(msg)
raise ClinicaCAPSError(error_message)
read_input_node.inputs.dartel_input_images = d_input
read_input_node.inputs.dartel_iteration_templates = dartel_iter_templates
if len(self.subjects):
print_images_to_process(self.subjects, self.sessions)
self.connect([(read_input_node, self.input_node,
[('dartel_input_images', 'dartel_input_images')]),
(read_input_node, self.input_node,
[('dartel_iteration_templates',
'dartel_iteration_templates')])])
def build_input_node(self):
"""Build and connect an input node to the pipeline."""
import os
import sys
from colorama import Fore
import nipype.pipeline.engine as npe
import nipype.interfaces.utility as nutil
from clinica.utils.inputs import clinica_file_reader
from clinica.utils.input_files import t1_volume_dartel_input_tissue
from clinica.utils.exceptions import ClinicaException
from clinica.utils.stream import cprint
from clinica.utils.ux import print_groups_in_caps_directory, print_images_to_process, print_begin_image
representative_output = os.path.join(
self.caps_directory, 'groups',
'group-' + self.parameters['group_label'], 't1',
'group-' + self.parameters['group_label'] + '_template.nii.gz')
if os.path.exists(representative_output):
cprint(
"%sDARTEL template for %s already exists. Currently, Clinica does not propose to overwrite outputs "
"for this pipeline.%s" %
(Fore.YELLOW, self.parameters['group_label'], Fore.RESET))
print_groups_in_caps_directory(self.caps_directory)
sys.exit(0)
# Check that there is at least 2 subjects
if len(self.subjects) <= 1:
raise ClinicaException(
'%sThis pipeline needs at least 2 images to create DARTEL template but '
'Clinica only found %s.%s' %
(Fore.RED, len(self.subjects), Fore.RESET))
read_parameters_node = npe.Node(name="LoadingCLIArguments",
interface=nutil.IdentityInterface(
fields=self.get_input_fields(),
mandatory_inputs=True))
all_errors = []
d_input = []
for tissue_number in self.parameters['dartel_tissues']:
try:
current_file = clinica_file_reader(
self.subjects, self.sessions, self.caps_directory,
t1_volume_dartel_input_tissue(tissue_number))
d_input.append(current_file)
except ClinicaException as e:
all_errors.append(e)
# Raise all errors if some happened
if len(all_errors) > 0:
error_message = 'Clinica faced errors while trying to read files in your BIDS or CAPS directories.\n'
for msg in all_errors:
error_message += str(msg)
raise RuntimeError(error_message)
# d_input is a list of size len(self.parameters['dartel_tissues'])
# Each element of this list is a list of size len(self.subjects)
read_parameters_node.inputs.dartel_inputs = d_input
if len(self.subjects):
print_images_to_process(self.subjects, self.sessions)
cprint(
'Computational time for DARTEL creation will depend on the number of images.'
)
print_begin_image('group-' + self.parameters['group_label'])
self.connect([(read_parameters_node, self.input_node,
[('dartel_inputs', 'dartel_input_images')])])
def build_input_node(self):
"""Build and connect an input node to the pipeline."""
import os
import sys
import nipype.interfaces.utility as nutil
import nipype.pipeline.engine as npe
from clinica.utils.exceptions import ClinicaException
from clinica.utils.input_files import t1_volume_dartel_input_tissue
from clinica.utils.inputs import clinica_file_reader
from clinica.utils.stream import cprint
from clinica.utils.ux import (
print_begin_image,
print_groups_in_caps_directory,
print_images_to_process,
)
representative_output = os.path.join(
self.caps_directory,
"groups",
f"group-{self.parameters['group_label']}",
"t1",
f"group-{self.parameters['group_label']}_template.nii.gz",
)
if os.path.exists(representative_output):
cprint(
msg=
(f"DARTEL template for {self.parameters['group_label']} already exists. "
"Currently, Clinica does not propose to overwrite outputs for this pipeline."
),
lvl="warning",
)
print_groups_in_caps_directory(self.caps_directory)
sys.exit(0)
# Check that there is at least 2 subjects
if len(self.subjects) <= 1:
raise ClinicaException(
"This pipeline needs at least 2 images to create DARTEL "
f"template but Clinica only found {len(self.subjects)}.")
read_parameters_node = npe.Node(
name="LoadingCLIArguments",
interface=nutil.IdentityInterface(fields=self.get_input_fields(),
mandatory_inputs=True),
)
all_errors = []
d_input = []
for tissue_number in self.parameters["dartel_tissues"]:
try:
current_file = clinica_file_reader(
self.subjects,
self.sessions,
self.caps_directory,
t1_volume_dartel_input_tissue(tissue_number),
)
d_input.append(current_file)
except ClinicaException as e:
all_errors.append(e)
# Raise all errors if some happened
if len(all_errors) > 0:
error_message = "Clinica faced errors while trying to read files in your BIDS or CAPS directories.\n"
for msg in all_errors:
error_message += str(msg)
raise RuntimeError(error_message)
# d_input is a list of size len(self.parameters['dartel_tissues'])
# Each element of this list is a list of size len(self.subjects)
read_parameters_node.inputs.dartel_inputs = d_input
if len(self.subjects):
print_images_to_process(self.subjects, self.sessions)
cprint(
"Computational time for DARTEL creation will depend on the number of images."
)
print_begin_image(f"group-{self.parameters['group_label']}")
# fmt: off
self.connect([(read_parameters_node, self.input_node,
[("dartel_inputs", "dartel_input_images")])])