Add option to save IMS file in a specified location

Author: lguerard

src/imcflibs/imagej/misc.py

@@ -669,7 +669,7 @@ def locate_latest_imaris(paths_to_check=None):
     return imaris_paths[-1]
 
 
-def run_imarisconvert(file_path, pixel_calibration=None):
+def run_imarisconvert(file_path, output_folder=None, pixel_calibration=None):
     """Convert a given file to Imaris format using ImarisConvert.
 
     Convert the input image file to Imaris format (Imaris5) using the
@@ -680,6 +680,8 @@ def run_imarisconvert(file_path, pixel_calibration=None):
     ----------
     file_path : str
         Absolute path to the input image file.
+    output_folder : str, optional
+        Folder where the newly created IMS file will be saved, by default None.
     pixel_calibration : tuple or list, optional
         Sequence of 3 values (x, y, z) representing voxel dimensions to be set during
         conversion, by default None.
@@ -693,9 +695,12 @@ def run_imarisconvert(file_path, pixel_calibration=None):
 
     imaris_path = locate_latest_imaris()
 
+    if not output_folder:
+        output_folder = os.getcwd()
+
     command = 'ImarisConvert.exe  -i "%s" -of Imaris5 -o "%s"' % (
         file_path,
-        file_path.replace(file_extension, ".ims"),
+        os.path.join(output_folder, file_path.replace(file_extension, ".ims")),
     )
     if pixel_calibration:
         command = command + " --voxelsizex %s --voxelsizey %s --voxelsizez %s" % (