From c88aa7932853b76a8ead3d80e1ce69980211b8ad Mon Sep 17 00:00:00 2001
From: s204159 <s204159@student.dtu.dk>
Date: Fri, 28 Jun 2024 09:53:01 +0200
Subject: [PATCH] Zarr cli
---
qim3d/io/convert.py | 3 ++-
qim3d/utils/cli.py | 40 +++++++++++++++++++++++++++++++++++-----
2 files changed, 37 insertions(+), 6 deletions(-)
diff --git a/qim3d/io/convert.py b/qim3d/io/convert.py
index f1981536..b2ab1e49 100644
--- a/qim3d/io/convert.py
+++ b/qim3d/io/convert.py
@@ -20,6 +20,7 @@ class Convert:
"""
self.chunk_shape = kwargs.get("chunk_shape", (64, 64, 64))
+
def convert(self, input_path, output_path):
# Stringify path in case it is not already a string
input_path = stringify_path(input_path)
@@ -30,7 +31,7 @@ class Convert:
if os.path.isfile(input_path):
match input_ext, output_ext:
case (".tif", ".zarr") | (".tiff", ".zarr"):
- return self.convert_tif_to_zarr(input_path, output_path)
+ return self.convert_tif_to_zarr(input_path, output_path, chunks=self.chunk_shape)
case _:
raise ValueError("Unsupported file format")
# Load a directory
diff --git a/qim3d/utils/cli.py b/qim3d/utils/cli.py
index 4b057142..ac8708c4 100644
--- a/qim3d/utils/cli.py
+++ b/qim3d/utils/cli.py
@@ -1,12 +1,12 @@
import argparse
import webbrowser
+import outputformat as ouf
from qim3d.gui import annotation_tool, data_explorer, iso3d, local_thickness
from qim3d.io.loading import DataLoader
from qim3d.utils import image_preview
from qim3d import __version__ as version
-import outputformat as ouf
-import qim3d
+import qim3d.io
QIM_TITLE = ouf.rainbow(
f"\n _ _____ __ \n ____ _(_)___ ___ |__ /____/ / \n / __ `/ / __ `__ \ /_ </ __ / \n/ /_/ / / / / / / /__/ / /_/ / \n\__, /_/_/ /_/ /_/____/\__,_/ \n /_/ v{version}\n\n",
@@ -14,6 +14,9 @@ QIM_TITLE = ouf.rainbow(
cmap="hot",
)
+def parse_tuple(arg):
+ # Remove parentheses if they are included and split by comma
+ return tuple(map(int, arg.strip('()').split(',')))
def main():
parser = argparse.ArgumentParser(description="Qim3d command-line interface.")
@@ -87,6 +90,30 @@ def main():
help="By default set the maximum value to be 255 so the contrast is strong. This turns it off.",
)
+ # File Convert
+ convert_parser = subparsers.add_parser(
+ "convert",
+ help="Convert files to different formats without loading the entire file into memory",
+ )
+ convert_parser.add_argument(
+ "input_path",
+ type=str,
+ metavar="Input path",
+ help="Path to image that will be converted",
+ )
+ convert_parser.add_argument(
+ "output_path",
+ type=str,
+ metavar="Output path",
+ help="Path to save converted image",
+ )
+ convert_parser.add_argument(
+ "--chunks",
+ type=parse_tuple,
+ metavar="Chunk shape",
+ default=(64,64,64),
+ help="Chunk size for the zarr file. Defaults to (64, 64, 64).",
+ )
args = parser.parse_args()
if args.subcommand == "gui":
@@ -104,13 +131,13 @@ def main():
else:
interface = iso3d.Interface()
interface.launch(inbrowser=inbrowser, force_light_mode=False)
-
+
elif args.annotation_tool:
if args.platform:
annotation_tool.run_interface(arghost)
else:
interface = annotation_tool.Interface()
- interface.launch(inbrowser=inbrowser, force_light_mode=False)
+ interface.launch(inbrowser=inbrowser, force_light_mode=False)
elif args.local_thickness:
if args.platform:
local_thickness.run_interface(arghost)
@@ -118,7 +145,6 @@ def main():
interface = local_thickness.Interface()
interface.launch(inbrowser=inbrowser, force_light_mode=False)
-
elif args.subcommand == "viz":
if not args.source:
print("Please specify a source file using the argument --source")
@@ -139,6 +165,7 @@ def main():
elif args.subcommand == "preview":
image = DataLoader().load(args.filename)
+
image_preview(
image,
image_width=args.resolution,
@@ -147,6 +174,9 @@ def main():
relative_intensity=args.absolute_values,
)
+ elif args.subcommand == "convert":
+ qim3d.io.convert(args.input_path, args.output_path, chunk_shape=args.chunks)
+
elif args.subcommand is None:
print(QIM_TITLE)
welcome_text = (
--
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