♻️ Import global Nipype loggers

CPAC/_entrypoints/run.py

@@ -28,7 +28,6 @@
 from warnings import simplefilter
 
 import yaml
-from nipype import logging
 
 from CPAC import __version__, license_notice
 from CPAC.pipeline import AVAILABLE_PIPELINE_CONFIGS
@@ -48,11 +47,10 @@
     upgrade_pipeline_to_1_8,
 )
 from CPAC.utils.docs import DOCS_URL_PREFIX
-from CPAC.utils.monitoring import failed_to_start, log_nodes_cb
+from CPAC.utils.monitoring import failed_to_start, FMLOGGER, log_nodes_cb, WFLOGGER
 from CPAC.utils.utils import update_nested_dict
 
 simplefilter(action="ignore", category=FutureWarning)
-logger = logging.getLogger("nipype.workflow")
 DEFAULT_TMP_DIR = "/tmp"
 
 
@@ -477,7 +475,7 @@ def run_main():
         if not args.group_file or not os.path.exists(args.group_file):
             import pkg_resources as p
 
-            logger.warning("\nNo group analysis configuration file was supplied.\n")
+            WFLOGGER.warning("\nNo group analysis configuration file was supplied.\n")
 
             args.group_file = p.resource_filename(
                 "CPAC",
@@ -493,11 +491,11 @@ def run_main():
                 if not os.path.exists(output_group):
                     shutil.copyfile(args.group_file, output_group)
             except (Exception, IOError):
-                logger.warning(
+                FMLOGGER.warning(
                     "Could not create group analysis configuration file.\nPlease refer to the C-PAC documentation for group analysis setup."
                 )
             else:
-                logger.warning(
+                WFLOGGER.warning(
                     "Please refer to the output directory for a template of  the file and, after customizing to your analysis, add the flag\n\n    --group_file %s\n\nto your `docker run` command\n",
                     output_group,
                 )
@@ -507,7 +505,7 @@ def run_main():
         else:
             import CPAC.pipeline.cpac_group_runner as cgr
 
-            logger.info(
+            WFLOGGER.info(
                 "Starting group level analysis of data in %s using %s",
                 bids_dir,
                 args.group_file,
@@ -537,14 +535,14 @@ def run_main():
         # validate input dir (if skip_bids_validator is not set)
         if not args.data_config_file:
             if args.bids_validator_config:
-                logger.info("Running BIDS validator...")
+                WFLOGGER.info("Running BIDS validator...")
                 run(f"bids-validator --config {args.bids_validator_config} {bids_dir}")
             elif args.skip_bids_validator:
-                logger.info("Skipping BIDS validator...")
+                WFLOGGER.info("Skipping BIDS validator...")
             elif bids_dir_is_s3:
-                logger.info("Skipping BIDS validator for S3 datasets...")
+                WFLOGGER.info("Skipping BIDS validator for S3 datasets...")
             else:
-                logger.info("Running BIDS validator...")
+                WFLOGGER.info("Running BIDS validator...")
                 run(f"bids-validator {bids_dir}")
 
         if args.preconfig:
@@ -560,7 +558,7 @@ def run_main():
         if "pipeline_setup" not in c:
             _url = f"{DOCS_URL_PREFIX}/user/pipelines/1.7-1.8-nesting-mappings"
 
-            logger.warning(
+            WFLOGGER.warning(
                 "\nC-PAC changed its pipeline configuration "
                 "format in v1.8.0.\nSee %s for details.\n",
                 _url,
@@ -711,7 +709,7 @@ def run_main():
                 output_dir, "working"
             )
         else:
-            logger.warning(
+            FMLOGGER.warning(
                 "Cannot write working directory to S3 bucket. "
                 "Either change the output directory to something "
                 "local or turn off the --save_working_dir flag"
@@ -733,19 +731,21 @@ def run_main():
             ]["calculate_motion_after"] = True
 
         if args.participant_label:
-            logger.info("#### Running C-PAC for %s", ", ".join(args.participant_label))
+            WFLOGGER.info(
+                "#### Running C-PAC for %s", ", ".join(args.participant_label)
+            )
         else:
-            logger.info("#### Running C-PAC")
+            WFLOGGER.info("#### Running C-PAC")
 
-        logger.info(
+        WFLOGGER.info(
             "Number of participants to run in parallel: %s",
             c["pipeline_setup", "system_config", "num_participants_at_once"],
         )
 
         if not args.data_config_file:
-            logger.info("Input directory: %s", bids_dir)
+            WFLOGGER.info("Input directory: %s", bids_dir)
 
-        logger.info(
+        WFLOGGER.info(
             "Output directory: %s\nWorking directory: %s\nLog directory: %s\n"
             "Remove working directory: %s\nAvailable memory: %s (GB)\n"
             "Available threads: %s\nNumber of threads for ANTs: %s",
@@ -805,7 +805,7 @@ def run_main():
                 args.participant_ndx = os.environ["AWS_BATCH_JOB_ARRAY_INDEX"]
 
             if 0 <= participant_ndx < len(sub_list):
-                logger.info(
+                WFLOGGER.info(
                     "Processing data for participant %s (%s)",
                     args.participant_ndx,
                     sub_list[participant_ndx]["subject_id"],
@@ -884,7 +884,7 @@ def run_main():
                     TypeError,
                     ValueError,
                 ) as e:
-                    logger.warning(
+                    WFLOGGER.warning(
                         "The run will continue without monitoring. Monitoring was configured to be enabled, but the monitoring server failed to start, so : %s\n",
                         e,
                     )
@@ -916,7 +916,7 @@ def run_main():
                     ],
                 }
 
-            logger.info("Starting participant level processing")
+            WFLOGGER.info("Starting participant level processing")
             exitcode = CPAC.pipeline.cpac_runner.run(
                 data_config_file,
                 pipeline_config_file,
@@ -931,7 +931,7 @@ def run_main():
 
             if args.analysis_level == "test_config":
                 if exitcode == 0:
-                    logger.info(
+                    WFLOGGER.info(
                         "\nPipeline and data configuration files should"
                         " have been written to %s and %s respectively.\n",
                         pipeline_config_file,
@@ -942,7 +942,7 @@ def run_main():
             from CPAC.utils.monitoring import LOGTAIL
 
             for warning in LOGTAIL["warnings"]:
-                logger.warning("%s\n", warning.rstrip())
+                WFLOGGER.warning("%s\n", warning.rstrip())
 
     sys.exit(exitcode)
 

CPAC/anat_preproc/utils.py

@@ -463,12 +463,9 @@ def normalize_wmparc(source_file, target_file, xfm, out_file):
 
 
 """This module provides interfaces for workbench -volume-remove-islands commands"""
-from nipype import logging
 from nipype.interfaces.base import CommandLineInputSpec, File, TraitedSpec
 from nipype.interfaces.workbench.base import WBCommand
 
-iflogger = logging.getLogger("nipype.interface")
-
 
 class VolumeRemoveIslandsInputSpec(CommandLineInputSpec):
     in_file = File(

CPAC/connectome/connectivity_matrix.py

@@ -22,14 +22,13 @@
 
 import numpy as np
 from nilearn.connectome import ConnectivityMeasure
-from nipype import logging
 from nipype.interfaces import utility as util
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
 from CPAC.utils.interfaces.function import Function
 from CPAC.utils.interfaces.netcorr import NetCorr, strip_afni_output_header
+from CPAC.utils.monitoring import IFLOGGER
 
-logger = logging.getLogger("nipype.workflow")
 connectome_methods = {
     "afni": {"Pearson": "", "Partial": "-part_corr"},
     "nilearn": {"Pearson": "correlation", "Partial": "partial correlation"},
@@ -85,8 +84,8 @@ def get_connectome_method(method, tool):
     cm_method = connectome_methods[tool.lower()].get(method, NotImplemented)
     if cm_method is NotImplemented:
         warning_message = f"{method} has not yet been implemented for {tool} in C-PAC."
-        if logger:
-            logger.warning(NotImplementedError(warning_message))
+        if IFLOGGER:
+            IFLOGGER.warning(NotImplementedError(warning_message))
         else:
             warn(warning_message, category=Warning)
     return cm_method

CPAC/func_preproc/func_ingress.py

@@ -14,12 +14,8 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-from nipype import logging
-
 from CPAC.utils.datasource import create_func_datasource, ingress_func_metadata
 
-logger = logging.getLogger("nipype.workflow")
-
 
 def connect_func_ingress(
     workflow, strat_list, c, sub_dict, subject_id, input_creds_path, unique_id=None

CPAC/func_preproc/func_preproc.py

@@ -16,10 +16,7 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 """Functional preprocessing."""
 # pylint: disable=ungrouped-imports,wrong-import-order,wrong-import-position
-from nipype import logging
 from nipype.interfaces import afni, ants, fsl, utility as util
-
-logger = logging.getLogger("nipype.workflow")
 from nipype.interfaces.afni import preprocess, utils as afni_utils
 
 from CPAC.func_preproc.utils import nullify

CPAC/image_utils/tests/test_smooth.py

@@ -25,7 +25,7 @@
 import CPAC.utils.test_init as test_utils
 from CPAC.utils.test_mocks import configuration_strategy_mock
 
-logger = getLogger("nipype.workflow")
+logger = getLogger("CPAC.image_utils.tests")
 basicConfig(format="%(message)s", level=INFO)
 
 

CPAC/isc/isc.py

@@ -17,11 +17,9 @@
 import numpy as np
 
 from CPAC.utils import correlation
-from CPAC.utils.monitoring.custom_logging import getLogger
+from CPAC.utils.monitoring import IFLOGGER
 from .utils import p_from_null, phase_randomize
 
-logger = getLogger("nipype.workflow")
-
 
 def isc(D, std=None, collapse_subj=True):
     assert D.ndim == 3
@@ -65,7 +63,7 @@ def isc_significance(ISC, min_null, max_null, two_sided=False):
 
 
 def isc_permutation(permutation, D, masked, collapse_subj=True, random_state=0):
-    logger.info("Permutation %s", permutation)
+    IFLOGGER.info("Permutation %s", permutation)
     min_null = 1
     max_null = -1
 

CPAC/isc/isfc.py

@@ -17,11 +17,9 @@
 import numpy as np
 
 from CPAC.utils import correlation
-from CPAC.utils.monitoring.custom_logging import getLogger
+from CPAC.utils.monitoring import IFLOGGER
 from .utils import p_from_null, phase_randomize
 
-logger = getLogger("nipype.workflow")
-
 
 def isfc(D, std=None, collapse_subj=True):
     assert D.ndim == 3
@@ -67,7 +65,7 @@ def isfc_significance(ISFC, min_null, max_null, two_sided=False):
 
 
 def isfc_permutation(permutation, D, masked, collapse_subj=True, random_state=0):
-    logger.info("Permutation %s", permutation)
+    IFLOGGER.info("Permutation %s", permutation)
     min_null = 1
     max_null = -1
 

CPAC/longitudinal_pipeline/longitudinal_preproc.py

@@ -26,11 +26,9 @@
 import nipype.interfaces.utility as util
 
 from CPAC.pipeline import nipype_pipeline_engine as pe
-from CPAC.utils.monitoring.custom_logging import getLogger
+from CPAC.utils.monitoring import IFLOGGER
 from CPAC.utils.nifti_utils import nifti_image_input
 
-logger = getLogger("nipype.workflow")
-
 
 def read_ants_mat(ants_mat_file):
     """Read a matrix, returning (translation) and (other transformations) matrices."""
@@ -162,7 +160,7 @@ def template_convergence(
         msg = f"template_convergence: matrix type {mat_type} does not exist"
         raise ValueError(msg)
     distance = norm_transformations(translation, oth_transform)
-    logger.info("distance = %s", abs(distance))
+    IFLOGGER.info("distance = %s", abs(distance))
 
     return abs(distance) <= convergence_threshold
 
@@ -451,7 +449,7 @@ def template_creation_flirt(
         convergence_threshold = np.finfo(np.float64).eps
 
     if len(input_brain_list) == 1 or len(input_skull_list) == 1:
-        logger.warning(
+        IFLOGGER.warning(
             "input_brain_list or input_skull_list contains only 1 image, "
             "no need to calculate template"
         )

CPAC/longitudinal_pipeline/longitudinal_workflow.py

@@ -17,7 +17,6 @@
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
 import os
 
-from nipype import logging
 from nipype.interfaces import fsl
 import nipype.interfaces.io as nio
 from indi_aws import aws_utils
@@ -47,8 +46,6 @@
 from CPAC.utils.strategy import Strategy
 from CPAC.utils.utils import check_config_resources, check_prov_for_regtool
 
-logger = logging.getLogger("nipype.workflow")
-
 
 @nodeblock(
     name="mask_T1w_longitudinal_template",

CPAC/network_centrality/pipeline.py

@@ -14,7 +14,6 @@
 
 # You should have received a copy of the GNU Lesser General Public
 # License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
-from nipype import logging
 from nipype.interfaces import fsl
 
 from CPAC.network_centrality.network_centrality import create_centrality_wf
@@ -23,8 +22,6 @@
 from CPAC.pipeline.nodeblock import nodeblock
 from CPAC.pipeline.schema import valid_options
 
-logger = logging.getLogger("nipype.workflow")
-
 
 def connect_centrality_workflow(
     workflow,

CPAC/network_centrality/utils.py

@@ -24,11 +24,9 @@
 from CPAC.pipeline.schema import valid_options
 from CPAC.utils.docs import docstring_parameter
 from CPAC.utils.interfaces.function import Function
-from CPAC.utils.monitoring.custom_logging import getLogger
+from CPAC.utils.monitoring import IFLOGGER
 from CPAC.utils.typing import ITERABLE, LIST
 
-logger = getLogger("nipype.workflow")
-
 
 def convert_pvalue_to_r(datafile, p_value, two_tailed=False):
     """
@@ -395,7 +393,7 @@ class ThresholdError(ValueError):
     def __init__(self, threshold_option, threshold):
         self.threshold_option = threshold_option
         self.threshold = threshold
-        logger.error("%s", type(threshold))
+        IFLOGGER.error("%s", type(threshold))
         self.message = f"For '{threshold_option}', threshold value must be "
         if threshold_option in ("Significance threshold", "Sparsity threshold"):
             self.message += "a positive number greater than 0 "