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Add option to save IMS file in a specified location #100

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Add option to save IMS file in a specified location #100

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9 changes: 7 additions & 2 deletions src/imcflibs/imagej/misc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -669,7 +669,7 @@
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
Expand All @@ -680,6 +680,8 @@
----------
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.
Expand All @@ -693,9 +695,12 @@

imaris_path = locate_latest_imaris()

if not output_folder:
output_folder = os.getcwd()

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src/imcflibs/imagej/misc.py#L698-L699 

Added lines #L698 - L699 were not covered by tests

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" % (
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