add convertor to transform zarr back to micro-manager folder format

ditb/commands/convert.py

@@ -6,7 +6,7 @@ This file is part of DITB.
 Contains the cli interface for the convert command
 """
 import click
-from ..io.converter import MM2Zarr
+from ..io.converter import MM2Zarr, mmzarr2MMformat
 from pathlib import Path
 import shutil
 
@@ -14,16 +14,16 @@ import shutil
 @click.argument('source', nargs=-1, type=click.Path(exists=True))
 @click.option('--destination', type=click.Path(exists=False),
                default = './processed',
-               help = "The destination folder to store converted data. The default value is a folder called ./processed")
-@click.option('--convertor', type=click.Choice(['MMtoZARR', 'ZARRtoHDF', 'ZARRtoTif'], case_sensitive=False),
-              help="Set the convertor to use", default = 'MMtoZARR')
+               help = "The destination folder to store converted data. The default value is a folder called: ./processed if MM2ZARR convertor is used. ./back_to_MM if ZARR2MM convertor is used")
+@click.option('--convertor', type=click.Choice(['MM2ZARR', 'ZARR2MM', 'ZARR2HDF', 'ZARR2Tif'], case_sensitive=False),
+              help="Set the convertor to use", default = 'MM2ZARR')
 @click.option('--force', is_flag=True, help="Force convert even if the directory is already in the destination folder")
 def convert(convertor, source, destination, force):
     """
     📦 Convert data to several format.
     """
 
-    if convertor in ['ZARRtoHDF', 'ZARRtoTif']:
+    if convertor in ['ZARR2HDF', 'ZARR2Tif']:
         raise NotImplementedError(f'This convertor {convertor} is not yet implemented, please be patient')
 
     # Create the destination folder if it does not exist
@@ -31,12 +31,13 @@ def convert(convertor, source, destination, force):
     destination = destination.expanduser()
     destination.mkdir(exist_ok=True)
 
+
+    if convertor == 'MM2ZARR':
         print(f'🪩 Use {convertor} to convert data to {destination} folder')
-    if convertor == 'MMtoZARR':
         for filein in source:
             if destination.name != filein:
                 # Create the output name
-                output_file = Path(destination) / (Path(filein).name + '.zarr')
+                output_file = destination / (Path(filein).name + '.zarr')
                 print(f'\n▷ convert {filein} to {output_file}')
 
                 if force:
@@ -58,7 +59,43 @@ def convert(convertor, source, destination, force):
                             print(f'Error for file {filein}')
                             print(e)
 
+    if convertor == 'ZARR2MM':
 
-    print('\n🪩 Done 🌟🌟🌟')
+        # Change de default destination ./processed to './back_to_MM'
+        if destination.name == 'processed':
+            destination = destination.parent / 'back_to_MM'
+
+        print(f'🪩 Use {convertor} to convert data to {destination} folder')
+
+        for filein in source:
 
+            # Check that the destination folder is not in the input files liste
+            # and that the file end by .zarr
+            fin = Path(filein)
+            if destination.name != filein and fin.suffix == '.zarr':
 
+                # Create the output destination for this file
+                output_dir = destination / fin.name.replace(fin.suffix, '')
+                print(f'\n▷ convert {filein} to {output_dir}')
+
+                if force:
+
+                    # Remove the directory if it exists
+                    if output_dir.is_dir():
+                        shutil.rmtree(str(output_dir))
+                    try:
+                        mmzarr2MMformat(filein, output_dir)
+                    except Exception as e:
+                        print(f'Error for file {filein}')
+                        print(e)
+
+                else:
+                    if not output_dir.is_dir():
+                        try:
+                            mmzarr2MMformat(filein, output_dir)
+                        except Exception as e:
+                            print(f'Error for file {filein}')
+                            print(e)
+
+
+    print('\n🪩 Done 🌟🌟🌟')

ditb/io/converter.py

@@ -8,10 +8,20 @@ from pathlib import Path
 from ome_zarr.writer import write_image
 from ome_zarr.io import parse_url
 from tqdm import tqdm
+import dask
+from dask.diagnostics import ProgressBar
+from tifffile import imwrite
 
 from .metadata import (make_global_metadata, get_pixel_size, get_roi_name_indices, reshapeMetadata,
-                       imagej_style_metadata, omero_style_metadata)
-from .imread import mmread
+                       imagej_style_metadata, omero_style_metadata, read_mmzarr_metadata, get_dimensions)
+from .imread import mmread, mmzarr_read
+
+try:
+    import orjson as json
+    orjson = True
+except Exception:
+    import json
+    orjson = False
 
 
 def MM2Zarr(mm_root_folder: str, destination_folder: str):
@@ -88,3 +98,56 @@ def MM2Zarr(mm_root_folder: str, destination_folder: str):
                                         'version': str(__version)}
 
 
+def mmzarr2MMformat(zarr_folder: str, destinatin_folder: str):
+    """
+    Convert mmzarr dataset back to micromanager format
+    """
+
+    @dask.delayed
+    def write_position(file_name, image, metadata=None, resolution=None, imagej=True) -> None:
+        """
+        Simple function to write a single tiff file with resolution information
+        """
+        imwrite(file_name, image, imagej=imagej, resolution=resolution, metadata=metadata)
+
+    zarr_folder = Path(zarr_folder)
+    data = mmzarr_read(zarr_folder)
+    meta = read_mmzarr_metadata(zarr_folder)
+    dims = get_dimensions(meta)
+
+    dest_folder = Path(destinatin_folder)
+    dest_folder.mkdir(parents=True, exist_ok=True)
+    pxsize = get_pixel_size(meta)
+    resolution = (1/pxsize, 1/pxsize)
+
+    write_operations = []
+    ## Micromanager images and metadata are grouped in all images in one folder per position
+    for ir, r in enumerate(meta['_roi_tiles']):
+        roi = r.capitalize()
+        for it, tile in enumerate(meta['_roi_tiles'][r]):
+            mm_meta_format = {'Summary': meta['Summary']}
+            for t in range(dims['time']):
+                for c in range(dims['channel']):
+                    for z in range(dims['z']):
+                        im_coord = meta[f'{roi}/Tile{it}'][t,c,z]['coords']
+                        im_meta =  meta[f'{roi}/Tile{it}'][t,c,z]['metadata']
+                        mm_meta_format[f'Coords-{im_meta["FileName"]}'] = im_coord
+                        mm_meta_format[f'Metadata-{im_meta["FileName"]}'] = im_meta
+
+                        # Create the parent folder if it does not exist
+                        outfile = dest_folder / Path(im_meta['FileName'])
+                        outfile.parent.mkdir(exist_ok=True)
+
+                        write_operations += [
+                            write_position(outfile, data[it, t, c, z], resolution=resolution, imagej=True)
+                        ]
+
+            with open(outfile.parent / 'metadata.txt', 'wb') as f:
+                if orjson:
+                    f.write(json.dumps(mm_meta_format, option=json.OPT_INDENT_2 | json.OPT_APPEND_NEWLINE))
+                else:
+                    f.write(json.dumps(mm_meta_format, indent=1, ensure_ascii=True))
+
+    # Run the task graph of Dask (delayed image operations on new_image_stack: load images, process, save)
+    with ProgressBar():
+        dask.compute(write_operations)

ditb/io/imwrite.py

@@ -13,13 +13,17 @@ from pathlib import Path
 from shutil import copy2
 import dask
 from dask.diagnostics import ProgressBar
-from .metadata import get_pixel_size, list_images
+from tifffile.tifffile import read_mm_header
+
+from ditb.io.imread import mmzarr_read
+from .metadata import get_pixel_size, list_images, read_mmzarr_metadata, get_dimensions
 from ome_zarr.writer import write_image
 from ome_zarr.io import parse_url
 from tqdm import tqdm
 import zarr
 
 
+
 def write_mmformat(source_root_folder: str, destination_root_folder: str,
                    global_metadata: dict, new_image_stack: np.array) -> None:
     """

ditb/io/metadata.py

@@ -688,3 +688,13 @@ def stack_info(metadata: dict):
     channels = get_channel_names(metadata)
 
     return f'-camera roi: {roi}\n-channels: {channels}'
+
+def read(folder_path: str):
+    """
+    Read metadata either from micromanager folder format or from a mmzarr format
+    """
+
+    if Path(folder_path).suffix == '.zarr':
+        return read_mmzarr_metadata(folder_path)
+    else:
+        return make_global_metadata(folder_path)

ditb/utils/colors.py

@@ -82,3 +82,12 @@ def channelName2Color(channel_name: str):
         return wavelength_to_hex(wmean)
     
     return '#ffffff'
+
+
+def merge_channels(dask_array, pixel_size):
+    """
+    Use the microfilm lib to create RGB merged color image
+    TODO
+    """
+
+    pass
\ No newline at end of file

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "DITB"
-version = "20240701rc3"
+version = "20240916rc1"
 readme = "README.md"
 requires-python = ">=3.11"
 authors = [{ name = "Hugo Chauvet", email = "hugo.chauvet@synchrotron-soleil.fr" }]