fix error message and remove pydeface from default conda env

UNFmontreal · Jun 18, 2024 · 83ede5a · 83ede5a
1 parent 9ae71ff
commit 83ede5a
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Showing 3 changed files with 26 additions and 13 deletions.
diff --git a/dcm2bids/dcm2bids_gen.py b/dcm2bids/dcm2bids_gen.py
@@ -123,16 +123,19 @@ def run(self):
 
         if self.bids_validate:
             try:
-                self.logger.info(f"Validate if {self.bids_dir} is BIDS valid.")
-                bids_version = run_shell_command(['bids-validator', '-v'])
-                self.logger.info(f"Use bids-validator version: {bids_version.decode()}")
+                self.logger.info(f"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("The bids-validator does not seem to work properly. "
+                self.logger.error("\033[91m"
+                                  "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.")
+                                  "https://github.com/bids-standard/bids-validator."
+                                  "\033[0m")
 
     def move(self, acq, idList, post_op):
         """Move an acquisition to BIDS format"""
@@ -187,9 +190,19 @@ def move(self, acq, idList, post_op):
                             else:
                                 cmd = cmd.replace('dst_file', str(dstFile))
 
-                            std_out = run_shell_command(cmd.split())
-                            self.logger.debug(std_out.decode())
-                            continue
+                            try:
+                                std_out = run_shell_command(cmd.split())
+                                self.logger.debug(f"Log from: {cmd}")
+                                self.logger.debug(std_out.decode())
+                                self.logger.info("")
+                                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")
 
             if ".json" in ext:
                 data = acq.dstSidecarData(idList)

diff --git a/dcm2bids/dcm2niix_gen.py b/dcm2bids/dcm2niix_gen.py
@@ -143,11 +143,12 @@ def execute(self):
                     self.logger.info("Temporary dicom directory removed.")
 
                 if "Warning" in output or "Error" in output:
-                    self.logger.info(f"\n{output}")
+                    self.logger.info("Log from dcm2niix execution")
+                    self.logger.info(f"\033[93m{output}\033[0m")
                 else:
                     self.logger.debug(f"\n{output}")
-
-                self.logger.info("Check log file for dcm2niix output\n")
+                    self.logger.info("Check log file for dcm2niix output\n")
+
 
         else:
             for dicomDir in self.dicom_dirs:

diff --git a/environment.yml b/environment.yml
@@ -5,5 +5,4 @@ channels:
   - HCC
 dependencies:
   - fsl-bet2
-  - fsl-flirt
-  - pydeface
+  - fsl-flirt