wip: experimenting with a command to upload the images

requirements.txt

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+click
+numpy
+cloud-volume
+tinybrain
+Pillow

setup.cfg

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+[metadata]
+name = tem2ng
+url = https://github.com/seung-lab/tem2ng/
+summary = Convert raw microscope images into a neuroglancer volume.
+description-content-type = text/markdown
+description-file = README.md
+author = William Silversmith
+author-email = [email protected]
+home-page = https://github.com/seung-lab/tem2ng/
+license = License :: OSI Approved :: BSD License
+classifier =
+    Intended Audience :: Developers
+    Development Status :: 4 - Beta
+    License :: OSI Approved :: BSD License
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Topic :: Software Development :: Libraries :: Python Modules
+
+[global]
+setup-hooks = pbr.hooks.setup_hook
+
+[files]
+packages = 
+    tem2ng
+
+[extras]

setup.py

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+import os
+import setuptools
+import sys
+
+setuptools.setup(
+  setup_requires=['pbr'],
+  python_requires="~=3.7", # >= 3.7 < 4.0
+  include_package_data=True,
+  entry_points={
+    "console_scripts": [
+      "tem2ng=tem2ng:main"
+    ],
+  },
+  pbr=True
+)
+

tem2ng/__init__.py

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+import re
+import os
+
+import click
+
+from cloudvolume import CloudVolume
+import numpy as np
+import tinybrain
+
+from PIL import Image
+
+TILE_REGEXP = re.compile(r'tile_(\d+)_(\d+)\.bmp')
+
+def get_ng(tilename, z=0):
+	x_map = {4:0,5:1,6:2,3:0,0:1,7:2,2:0,1:1,8:2}
+	get_x = lambda t1,t2: 6000 * ((t1%25)*3 + x_map[t2])
+	y_map = {4:0,3:1,2:2,5:0,0:1,1:2,6:0,7:1,8:2}
+	get_y = lambda t1,t2: 6000 * ((t1//25)*3 + y_map[t2])
+
+	t1, t2 = re.match(TILE_REGEXP, tilename).groups()
+
+	x0 = get_x(t1, t2)
+	xf = x0 + 6000
+	y0 = get_y(t1,t2)
+	yf = y0 + 6000
+
+	return f"{x0}-{xf}_{y0}-{yf}_{z}-{z+1}"
+
+@click.command()
+@click.argument("source")
+def main(source):
+	cv = CloudVolume("matrix://pni-tem1/test/")
+
+	for filename in os.scandir(source):
+		ext = os.path.splitext(filename)[1]
+		if ext != ".bmp":
+			continue
+
+		img = Image.open(filename)
+
+
+	img = Image.open("tile_99_0.bmp")
+	img.show()
+
+
+
+
+
+
+
+
+
+