DM conversion flow

em_workflows.dm_conversion.flow.convert_dms_to_mrc(file_path: FilePath) → None

em_workflows.dm_conversion.flow.convert_if_int16_tiff(file_path: FilePath) → None: accepts a tiff Path obj tests if 16 bit if 16 bit convert (write to assets_dir) & return Path else return orig Path

em_workflows.dm_conversion.flow.convert_2d_mrc_to_tiff(file_path: FilePath) → None

Checks Projects dir for mrc inputs. We assume anything in Projects will be 2D. Converts to tiff file, 1024 in size (using constant LARGE_DIM)

env IMOD_OUTPUT_FORMAT=TIF newstack –shrink $shrink_factor$ -antialias 6 -mode 0 -meansd 140,50 f_in.mrc f_out.tif where shrink_factor is input_size/1024 used the smaller of x and y (4092/1024)

em_workflows.dm_conversion.flow.convert_dm_mrc_to_jpeg(file_path: FilePath) → None: converts previously generated mrc file, (derived from a dm file) to jpeg. note, ignores everything that’s NOT <name>dm_as_mrc.mrc that is, convert_dm_mrc_to_jpeg does not process ALL mrc files.

em_workflows.dm_conversion.flow.scale_jpegs(file_path: FilePath, size: str) → dict | None: generates keyThumbnail and keyImage looks for file names <something>_mrc_as_jpg.jpeg