answer Sam comments

Dockerfile

@@ -19,7 +19,7 @@ FROM debian:stable AS runtime
 COPY --from=build /venv /venv
 
 # Point to conda executables
-ENV PATH /venv/bin:$PATH
+ENV PATH="/venv/bin:$PATH"
 
 # Set FSL variables
 ENV FSLDIR="/venv" 
@@ -54,4 +54,4 @@ RUN pip install -e .
 
 RUN pip install pydeface
 
-ENTRYPOINT [""]
+ENTRYPOINT ["dcm2bids"]

dcm2bids/dcm2bids_gen.py

@@ -123,19 +123,17 @@ def run(self):
 
         if self.bids_validate:
             try:
-                self.logger.info(f"BIDS VALIDATION")
+                self.logger.info("BIDS VALIDATION")
                 bids_version = run_shell_command(['bids-validator', '-v'], False)
                 self.logger.info(f"Use bids-validator version: {bids_version.decode()[:-1]}")
                 bids_report = run_shell_command(['bids-validator', self.bids_dir])
                 self.logger.info("Report from bids-validator")
                 self.logger.info(bids_report.decode())
             except Exception:
-                self.logger.error("\033[91m"
-                                  "The bids-validator does not seem to work properly. "
+                self.logger.error("The bids-validator does not seem to work properly. "
                                   "The bids-validator may not be installed on your "
                                   "computer. Please check: "
-                                  "https://github.com/bids-standard/bids-validator."
-                                  "\033[0m")
+                                  "https://github.com/bids-standard/bids-validator.")
 
     def move(self, acq, idList, post_op):
         """Move an acquisition to BIDS format"""
@@ -198,11 +196,10 @@ def move(self, acq, idList, post_op):
                                 continue
                             except Exception:
                                 self.logger.error(
-                                  "\033[91m"
                                   f"The command post_op: \"{cmd}\" "
                                   "does not seem to work properly. "
                                   "Check if it is installed on your "
-                                  "computer.\033[0m\n")
+                                  "computer.\n")
 
             if ".json" in ext:
                 data = acq.dstSidecarData(idList)

dcm2bids/dcm2niix_gen.py

@@ -144,7 +144,10 @@ def execute(self):
 
                 if "Warning" in output or "Error" in output:
                     self.logger.info("Log from dcm2niix execution")
-                    self.logger.info(f"\033[93m{output}\033[0m")
+                    if "Warning" in output:
+                        self.logger.warning(f"{output}")
+                    else:
+                        self.logger.error(f"{output}")
                 else:
                     self.logger.debug(f"\n{output}")
                     self.logger.info("Check log file for dcm2niix output\n")

dcm2bids/utils/logger.py

@@ -19,7 +19,7 @@ def setup_logging(log_level, log_file=None):
 
     sh = logging.StreamHandler(sys.stdout)
     sh.setLevel(log_level)
-    sh_fmt = logging.Formatter(fmt="%(levelname)-8s| %(message)s")
+    sh_fmt = CustomFormatter(fmt="%(levelname)-8s| %(message)s")
     sh.setFormatter(sh_fmt)
 
     # default formatting is kept for the log file"
@@ -30,3 +30,30 @@ def setup_logging(log_level, log_file=None):
         datefmt="%Y-%m-%d %H:%M:%S",
         handlers=[fh, sh]
     )
+
+
+class CustomFormatter(logging.Formatter):
+    """Logging colored formatter, adapted from https://stackoverflow.com/a/56944256/3638629"""
+
+    grey = '\x1b[38;21m'
+    blue = '\x1b[38;5;39m'
+    yellow = '\x1b[38;5;226m'
+    red = '\x1b[38;5;196m'
+    bold_red = '\x1b[31;1m'
+    reset = '\x1b[0m'
+
+    def __init__(self, fmt):
+        super().__init__()
+        self.fmt = fmt
+        self.FORMATS = {
+            logging.DEBUG: self.grey + self.fmt + self.reset,
+            logging.INFO: self.blue + self.fmt + self.reset,
+            logging.WARNING: self.yellow + self.fmt + self.reset,
+            logging.ERROR: self.red + self.fmt + self.reset,
+            logging.CRITICAL: self.bold_red + self.fmt + self.reset
+        }
+
+    def format(self, record):
+        log_fmt = self.FORMATS.get(record.levelno)
+        formatter = logging.Formatter(log_fmt)
+        return formatter.format(record)

environment.yml

@@ -2,7 +2,6 @@ name: fsl
 channels:
   - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/
   - conda-forge
-  - HCC
 dependencies:
   - fsl-bet2
   - fsl-flirt