diff --git a/qim3d/io/convert.py b/qim3d/io/convert.py
index 09694d7822f63cfc10a85bec9ca58cbb59ce6b40..6568965e896dbe096db4c02e2e9dfc0a14e092d2 100644
--- a/qim3d/io/convert.py
+++ b/qim3d/io/convert.py
@@ -22,6 +22,7 @@ class Convert:
"""
self.chunk_shape = kwargs.get("chunk_shape", (64, 64, 64))
self.base_name = kwargs.get("base_name", None)
+ self.contains = kwargs.get("contains", None)
def convert(self, input_path, output_path):
def get_file_extension(file_path):
@@ -37,7 +38,10 @@ class Convert:
output_ext = get_file_extension(output_path)
output_path = stringify_path(output_path)
- if os.path.isfile(input_path) and os.path.isfile(output_path):
+ print("sdf", os.path.isdir(input_path) , input_ext, output_ext)
+
+
+ if os.path.isfile(input_path) and output_ext:
match input_ext, output_ext:
case (".tif", ".zarr") | (".tiff", ".zarr"):
return self.convert_tif_to_zarr(input_path, output_path)
@@ -45,11 +49,6 @@ class Convert:
return self.convert_nifti_to_zarr(input_path, output_path)
case _:
raise ValueError("Unsupported file format")
- elif os.path.isfile(input_path) and os.path.isdir(output_path):
- if input_ext == ".zarr" and not output_ext:
- return self.convert_zarr_to_tiff_stack(input_path, output_path)
- else:
- raise ValueError("Unsupported file format")
# Load a directory
elif os.path.isdir(input_path):
match input_ext, output_ext:
@@ -59,13 +58,14 @@ class Convert:
return self.convert_zarr_to_nifti(input_path, output_path)
case (".zarr", ".nii.gz"):
return self.convert_zarr_to_nifti(input_path, output_path, compression=True)
+ case (".zarr", ""):
+ print("1")
+ self.convert_zarr_to_tiff_stack(input_path, output_path)
+ case ("", ".zarr"):
+ print("2")
+ return self.convert_tiff_stack_to_zarr(input_path, output_path)
case _:
raise ValueError("Unsupported file format")
- elif os.path.isdir(input_path) and os.path.isfile(output_path):
- if not input_ext and output_ext == ".zarr":
- return self.convert_tiff_stack_to_zarr(input_path, output_path)
- else:
- raise ValueError("Unsupported file format")
# Fail
else:
# Find the closest matching path to warn the user
@@ -75,7 +75,7 @@ class Convert:
similar_paths = difflib.get_close_matches(input_path, valid_paths)
if similar_paths:
suggestion = similar_paths[0] # Get the closest match
- message = f"Invalid path. Did you mean '{suggestion}'?"
+ message = f"Invalid path '{input_path}'. Did you mean '{suggestion}'?"
raise ValueError(repr(message))
else:
raise ValueError("Invalid path")
@@ -141,7 +141,7 @@ class Convert:
zarr.core.Array: zarr array containing the data from the tiff stack
"""
# ! tiff stack memmap is stored as slices on disk and not as a single file, making assignments to blocks slow.
- vol = load(tiff_stack_path, virtual_stack=True)
+ vol = load(tiff_stack_path, virtual_stack=True, contains=self.contains)
return self._save_zarr(zarr_path, vol)
def convert_zarr_to_tiff_stack(self, zarr_path, tiff_stack_path):
@@ -184,7 +184,11 @@ class Convert:
save(nifti_path, z, compression=compression)
-def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64), base_name: str = None):
+def convert(input_path: str,
+ output_path: str,
+ chunk_shape: tuple = (64, 64, 64),
+ base_name: str = None,
+ contains: str = None):
"""Convert a file to another format without loading the entire file into memory
Args:
@@ -193,5 +197,7 @@ def convert(input_path: str, output_path: str, chunk_shape: tuple = (64, 64, 64)
chunk_shape (tuple, optional): chunk size for the zarr file. Defaults to (64, 64, 64).
base_name (str, optional): base name for the tiff stack. Defaults to None.
"""
- converter = Convert(chunk_shape=chunk_shape,base_name=base_name)
+ converter = Convert(chunk_shape=chunk_shape,
+ base_name=base_name,
+ contains=contains)
converter.convert(input_path, output_path)
diff --git a/qim3d/io/saving.py b/qim3d/io/saving.py
index b163c3126705962e0c437a50a86aeb28ed043254..f5b62b939c28e07668ec2243c257ad6d93a65cba 100644
--- a/qim3d/io/saving.py
+++ b/qim3d/io/saving.py
@@ -34,11 +34,13 @@ import tifffile
import zarr
from pydicom.dataset import FileDataset, FileMetaDataset
from pydicom.uid import UID
+from tqdm import tqdm
from qim3d.io.logger import log
from qim3d.utils.internal_tools import sizeof, stringify_path
+
class DataSaver:
"""Utility class for saving data to different file formats.
@@ -111,7 +113,7 @@ class DataSaver:
idx = [slice(None)] * data.ndim
# Iterate through each slice and save
- for i in range(no_slices):
+ for i in tqdm(range(no_slices)):
idx[self.sliced_dim] = i
sliced = data[tuple(idx)]
filename = self.basename + str(i).zfill(zfill_val) + extension
diff --git a/qim3d/utils/cli.py b/qim3d/utils/cli.py
index c22d6b134095b604da8df073fd70aa5b2ff373f3..d99e781b4a7126097c0f69be1642bd5b35bf3873 100644
--- a/qim3d/utils/cli.py
+++ b/qim3d/utils/cli.py
@@ -84,8 +84,9 @@ def main():
preview_parser = subparsers.add_parser('convert', help= 'Convert files to different formats without loading the entire file into memory')
preview_parser.add_argument('input_path',type = str, metavar = 'Input path', help = 'Path to image that will be converted')
preview_parser.add_argument('output_path',type = str, metavar = 'Output path', help = 'Path to save converted image')
- preview_parser.add_argument('chunk_shape',type = tuple, metavar = 'Chunk shape', help = 'Chunk size for the zarr file', default = (64,64,64))
- preview_parser.add_argument('base_name',type = str, metavar = 'Base name', help = 'Base name for the zarr file', default = None)
+ preview_parser.add_argument('--chunk_shape',type = tuple, metavar = 'Chunk shape', help = 'Chunk size for the zarr file', default = (64,64,64))
+ preview_parser.add_argument('--base_name',type = str, metavar = 'Base name', help = 'Base name for the zarr file', default = None)
+ preview_parser.add_argument('--contains',type = str, metavar = 'Contains', help = 'Part of the name that is common for the TIFF file stack', default = None)
args = parser.parse_args()
@@ -144,7 +145,14 @@ def main():
slice=args.slice,
relative_intensity=args.absolute_values,
)
-
+
+ elif args.subcommand == 'convert':
+ qim3d.io.convert(args.input_path,
+ args.output_path,
+ args.chunk_shape,
+ args.base_name,
+ args.contains)
+
elif args.subcommand is None:
welcome_text = (
"\n"
@@ -172,8 +180,7 @@ def main():
parser.print_help()
print("\n")
- elif args.subcommand == 'convert':
- qim3d.io.convert(args.input_path, args.output_path, args.chunk_shape, args.base_name)
+
if __name__ == "__main__":