working on getting the other images over (5476cdb4) · Commits · Elphel / image-compression

.gitignore

+2 −1

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		@@ -17,3 +17,4 @@ attic
		*.corr-xml
		*.DS_Store
		lwir16.tar.gz
		*.mp4
		No newline at end of file

ErrorImageCreator.py

+7 −7

Original line number	Diff line number	Diff line
		@@ -93,7 +93,7 @@ if __name__ == "__main__":
		list_dic = np.load("second_dic.npy", allow_pickle="TRUE")
		bins = [21,32,48]
		print(images)
		encoded_string2 = bytes_to_bitstring(read_from_file(images[3][:-5] + "_Compressed.txt"))
		encoded_string2 = bytes_to_bitstring(read_from_file(images[0][:-5] + "_Compressed.txt"))
		original_array, error_array = produce_error_array(encoded_string2, list_dic, bins, False)
		adjusted_errors = color_adjust(abs(error_array))
		original_array_adjusted = color_adjust(original_array)
		@@ -107,12 +107,12 @@ if __name__ == "__main__":



		encoded_string2 = bytes_to_bitstring(read_from_file(images[0][:-5] + "_Compressed.txt"))
		original_array, error_array = produce_error_array(encoded_string2, list_dic, bins, False)
		adjusted_errors = color_adjust(abs(error_array))
		original_array_adjusted = color_adjust(original_array)
		plt.subplot(133)
		plt.imshow(adjusted_errors,cmap = 'gray', vmin = 0, vmax=255)
		# encoded_string2 = bytes_to_bitstring(read_from_file(images[0][:-5] + "_Compressed.txt"))
		# original_array, error_array = produce_error_array(encoded_string2, list_dic, bins, False)
		# adjusted_errors = color_adjust(abs(error_array))
		# original_array_adjusted = color_adjust(original_array)
		# plt.subplot(133)
		# plt.imshow(adjusted_errors,cmap = 'gray', vmin = 0, vmax=255)

FullTester.ipynb

+7 −44

Original line number	Diff line number	Diff line
		%% Cell type:code id: tags:

		``` python
		from WorkingPyDemo import *
		from time import time
		from scipy import misc
		import imageio
		import png
		```

		%% Cell type:code id: tags:

		``` python
		scenes = file_extractor(folder_name)
		scenes = file_extractor("averaged_images(11)")
		images = image_extractor(scenes)
		print(len(images))
		newnamesforlater = []
		file_sizes_new = []
		file_sizes_old = []
		list_dic = np.load("first_dic.npy", allow_pickle="TRUE")
		bins = [21,32,48]
		for i in range(len(images)):

		if images[i][-5:] == ".tiff":
		newname = images[i][:-5]
		else:
		newname = images[i][:-4]
		if images[i][-18:] != "Compressedlzw.tiff":
		newnamesforlater.append(newname + "_Compressed.txt")
		# with open(newname + "_Compressed.txt", 'wb') as f:
		# f.write(inletters)
		file_sizes_new.append((os.path.getsize(newname + "_Compressed.txt")))
		file_sizes_old.append((os.path.getsize(newname + "RemovedFirstLine" + ".tif")))
		# file_sizes_old.append((os.path.getsize(newname + "RemovedFirstLine" + ".tif")))
		file_sizes_old.append((os.path.getsize(newname + ".tiff")))
		file_sizes_new.append(os.path.getsize("first_dic.npy"))
		print(len(newnamesforlater))
		print(np.sum(file_sizes_new)/np.sum(file_sizes_old))
		```

		%% Output

		264
		263
		0.40415934529931374
		3
		3
		0.5416965429002373

		%% Cell type:code id: tags:

		``` python
		for i, filename in enumerate(images):
		newimage = Image.open(filename)
		newimage = np.array(newimage)
		newimage = newimage[1:]
		newimage = Image.fromarray(newimage)
		newimage.save(filename[:-5]+ "RemovedFirstLine" + ".tif")
		```

		%% Cell type:code id: tags:

		``` python
		print(file_sizes_new[214]/file_sizes_old[214])
		print(np.max(file_sizes_new)/file_sizes_old[125])
		print((np.sum([file_sizes_new[0:16]]))/np.sum(file_sizes_old[0:16]))
		print((np.sum([file_sizes_new[0:16]]) + file_sizes_new[-1])/np.sum(file_sizes_old[0:16]))
		print(np.sum(file_sizes_new)/np.sum(file_sizes_old))
		print(np.sum(file_sizes_new[:-1])/np.sum(file_sizes_old))
		print((np.sum([file_sizes_new[0]]))/np.sum(file_sizes_old[0]))
		print((np.sum([file_sizes_new[0]])+ file_sizes_new[-1])/np.sum(file_sizes_old[0]))
		```

		%% Output

		0.3767853274384346
		0.4979190885485795
		0.3972905625173536
		0.41933998568991976
		0.40415934529931374
		0.4028230157727312
		0.39809636267662574
		0.750887133437684

		%% Cell type:code id: tags:

		``` python
		pngsizes = []
		for i, filename in enumerate(images):
		newimage = Image.open(filename)
		newimage = np.array(newimage)
		newimage = newimage[1:]
		with open(newnamesforlater[i][:-4] + ".png", 'wb') as f:
		writer = png.Writer(newimage.shape[1], newimage.shape[0], greyscale=True, bitdepth=16)
		writer.write(f, newimage)
		pngsizes.append(os.path.getsize(newnamesforlater[i][:-4] + ".png"))
		print(np.sum(pngsizes)/np.sum(file_sizes_old))
		```

		%% Output

		---------------------------------------------------------------------------
		error Traceback (most recent call last)
		/home/bryce/git/master/FullTester.ipynb Cell 5' in <cell line: 2>()
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000004?line=5'>6</a> with open(newnamesforlater[i][:-4] + ".png", 'wb') as f:
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000004?line=6'>7</a> writer = png.Writer(newimage.shape[1], newimage.shape[0], greyscale=True, bitdepth=16)
		----> <a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000004?line=7'>8</a> writer.write(f, newimage)
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000004?line=8'>9</a> pngsizes.append(os.path.getsize(newnamesforlater[i][:-4] + ".png"))
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000004?line=9'>10</a> print(np.sum(pngsizes)/np.sum(file_sizes_old))
		File ~/.local/lib/python3.8/site-packages/png.py:668, in Writer.write(self, outfile, rows)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=664'>665</a> a = array(fmt, itertools.chain(*check_rows(rows)))
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=665'>666</a> return self.write_array(outfile, a)
		--> <a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=667'>668</a> nrows = self.write_passes(outfile, check_rows(rows))
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=668'>669</a> if nrows != self.height:
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=669'>670</a> raise ProtocolError(
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=670'>671</a> "rows supplied (%d) does not match height (%d)" %
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=671'>672</a> (nrows, self.height))
		File ~/.local/lib/python3.8/site-packages/png.py:703, in Writer.write_passes(self, outfile, rows)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=699'>700</a> elif self.bitdepth == 16:
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=700'>701</a> rows = unpack_rows(rows)
		--> <a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=702'>703</a> return self.write_packed(outfile, rows)
		File ~/.local/lib/python3.8/site-packages/png.py:738, in Writer.write_packed(self, outfile, rows)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=734'>735</a> # raise i scope out of the for loop. set to -1, because the for loop
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=735'>736</a> # sets i to 0 on the first pass
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=736'>737</a> i = -1
		--> <a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=737'>738</a> for i, row in enumerate(rows):
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=738'>739</a> # Add "None" filter type.
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=739'>740</a> # Currently, it's essential that this filter type be used
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=740'>741</a> # for every scanline as
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=741'>742</a> # we do not mark the first row of a reduced pass image;
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=742'>743</a> # that means we could accidentally compute
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=743'>744</a> # the wrong filtered scanline if we used
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=744'>745</a> # "up", "average", or "paeth" on such a line.
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=745'>746</a> data.append(0)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=746'>747</a> data.extend(row)
		File ~/.local/lib/python3.8/site-packages/png.py:1001, in unpack_rows(rows)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=998'>999</a> for row in rows:
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=999'>1000</a> fmt = '!%dH' % len(row)
		-> <a href='file:///home/bryce/.local/lib/python3.8/site-packages/png.py?line=1000'>1001</a> yield bytearray(struct.pack(fmt, *row))
		error: required argument is not an integer
		0.6922330946285837

		%% Cell type:code id: tags:

		``` python
		pngsizes = []
		for i in range(19,20):
		newimage = Image.open(images[i])
		print(np.array(newimage))
		newimage = (np.array(newimage) - np.min(newimage)).astype(int)
		# newimage = newimage[1:]
		with open(newnamesforlater[i][:-4] + ".png", 'wb') as f:
		writer = png.Writer(newimage.shape[1], newimage.shape[0], greyscale=True, bitdepth=16)
		writer.write(f, newimage)
		pngsizes.append(os.path.getsize(newnamesforlater[i][:-4] + ".png"))
		print(np.sum(pngsizes)/file_sizes_old[19])
		```

		%% Output

		[[-190.26562 -177.99805 -177.38672 ... -166.95898 -156.64062 -145.72461]
		[-175.46094 -163.56055 -183.07617 ... -169.2207 -167.58789 -154.14062]
		[-171.45898 -179.1582 -174.68164 ... -173.10547 -157.51758 -156.97461]
		...
		[-143.66992 -127.69531 -143.9043 ... 156.90625 170.79102 165.55469]
		[-139.97656 -134.71875 -152.26953 ... 169.49805 158.11914 172.49023]
		[-145.33984 -127.59375 -134.07227 ... 182.88672 169.80273 183.32812]]
		0.3016682254469224

		%% Cell type:code id: tags:

		``` python
		print(os.path.getsize("1626032610_393963_0.xcf")/os.path.getsize("images/1626032610_393963/1626032610_393963_0.tiff"))
		```

		%% Output

		0.5676821409714287

		%% Cell type:code id: tags:

		``` python
		print(os.path.getsize("1626032610_393963_0.png")/os.path.getsize("images/1626032610_393963/1626032610_393963_0.tiff"))
		```

		%% Output

		0.4855910784741866

		%% Cell type:code id: tags:

		``` python
		for i, filename in enumerate(images):
		original = Image.open(filename)
		compressed = Image.open(newnamesforlater[i][:-4] + ".png")
		original = np.array(original)[1:]
		compressed = np.array(compressed)
		if not np.allclose(original, compressed):
		print(i)
		```

		%% Cell type:code id: tags:

		``` python
		print((np.sum(pngsizes))/np.sum(file_sizes_old))
		print((np.sum(pngsizes) - np.sum(file_sizes_new))/np.sum(pngsizes))
		```

		%% Output

		0.6120739575336334
		0.33712836894440124

		%% Cell type:code id: tags:

		``` python
		```

		%% Cell type:code id: tags:

		``` python
		from PIL import TiffTags
		TiffTags.LIBTIFF_CORE.add(318)
		```

		%% Cell type:code id: tags:

		``` python
		lwz_sizes = []
		for i, filename in enumerate(images):
		newimage = Image.open(filename)
		newimage = np.array(newimage)
		newimage = newimage[1:]
		print(newimage.dtype)
		newimage = Image.fromarray(newimage)
		newimage.save(newnamesforlater[i][:-4]+ "lzw" + ".tiff", compression='tiff_lzw', tiffinfo={317: 2})

		lwz_sizes.append(os.path.getsize(newnamesforlater[i][:-4]+ "lzw" + ".tiff"))
		print(np.sum(lwz_sizes)/np.sum(file_sizes_old))
		```

		%% Output

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		---------------------------------------------------------------------------
		KeyboardInterrupt Traceback (most recent call last)
		/home/bryce/git/master/FullTester.ipynb Cell 13' in <cell line: 2>()
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000011?line=5'>6</a> print(newimage.dtype)
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000011?line=6'>7</a> newimage = Image.fromarray(newimage)
		----> <a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000011?line=7'>8</a> newimage.save(newnamesforlater[i][:-4]+ "lzw" + ".tiff", compression='tiff_lzw', tiffinfo={317: 2})
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000011?line=9'>10</a> lwz_sizes.append(os.path.getsize(newnamesforlater[i][:-4]+ "lzw" + ".tiff"))
		<a href='vscode-notebook-cell:/home/bryce/git/master/FullTester.ipynb#ch0000011?line=10'>11</a> print(np.sum(lwz_sizes)/np.sum(file_sizes_old))
		File ~/.local/lib/python3.8/site-packages/PIL/Image.py:2300, in Image.save(self, fp, format, **params)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/Image.py?line=2296'>2297</a> fp = builtins.open(filename, "w+b")
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/Image.py?line=2298'>2299</a> try:
		-> <a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/Image.py?line=2299'>2300</a> save_handler(self, fp, filename)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/Image.py?line=2300'>2301</a> except Exception:
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/Image.py?line=2301'>2302</a> if open_fp:
		File ~/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py:1814, in _save(im, fp, filename)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py?line=1810'>1811</a> e.setimage(im.im, (0, 0) + im.size)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py?line=1811'>1812</a> while True:
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py?line=1812'>1813</a> # undone, change to self.decodermaxblock:
		-> <a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py?line=1813'>1814</a> l, s, d = e.encode(16 * 1024)
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py?line=1814'>1815</a> if not _fp:
		<a href='file:///home/bryce/.local/lib/python3.8/site-packages/PIL/TiffImagePlugin.py?line=1815'>1816</a> fp.write(d)
		KeyboardInterrupt:

		%% Cell type:code id: tags:

		``` python
		lwz_sizes = []
		for i in range(19,20):
		print(images[i])
		newimage = Image.open(images[i])
		newimage = np.array(newimage)
		newimage = newimage[1:]
		newimage = Image.fromarray(newimage)
		newimage.save(newnamesforlater[i][:-4]+ "lzw" + ".tiff", compression='tiff_lzw', tiffinfo={317: 2})

		lwz_sizes.append(os.path.getsize(newnamesforlater[i][:-4]+ "lzw" + ".tiff"))
		print(np.sum(lwz_sizes)/np.sum(file_sizes_old))
		```

		%% Output

		images/1626032610_393963/NoInterference.tiff
		0.005975943965048414

		%% Cell type:code id: tags:

		``` python
		print(np.sum(lwz_sizes)/file_sizes_old[19])
		```

		%% Output

		0.7888902959444759

		%% Cell type:code id: tags:

		``` python
		print((np.sum(lwz_sizes) - np.sum(file_sizes_new))/np.sum(lwz_sizes))
		```

		%% Output

		0.34492564114323154

		%% Cell type:code id: tags:

		``` python
		print(len(images))
		for i, item in enumerate(images):
		# print(item[-18:])
		if item[-18:] == "Compressedlzw.tiff":
		os.remove(item)
		scenes = file_extractor(folder_name)
		images = image_extractor(scenes)
		print(len(images))
		```

		%% Output

		263
		263

		%% Cell type:code id: tags:

		``` python
		def all_image_extractor(scenes):
		"""
		This function gives the list of all of the valid images
		Parameters:
		scenes (list): a list of all the files in the directory
		Returns:
		images (list): a list of all the images in the directory
		"""
		image_folder = []
		for scene in scenes:
		files = os.listdir(scene)
		for file in files:
		if file[-7:] == "_6.tiff":
		continue
		else:
		image_folder.append(os.path.join(scene, file))
		return image_folder #returns a list of file paths to .tiff files in the specified directory given in file_extractor
		```

		%% Cell type:code id: tags:

		``` python
		all_files = all_image_extractor(scenes)
		print(len(all_files))
		for i, item in enumerate(all_files):
		# print(item[-18:])
		print(item[-21:])
		if item[-21:] == "RemovedFirstLine.tiff":
		os.remove(item)
		scenes = file_extractor(folder_name)
		all_files = all_image_extractor(scenes)
		print(len(all_files))
		```

		%% Output

		1442
		13_Compressedlzw.tiff
		7803_3_Compressed.png
		7803_5_Compressed.png
		7803_1_Compressed.png
		_5_Compressedlzw.tiff
		803_14_Compressed.png
		2RemovedFirstLine.tif
		7803_8_Compressed.txt
		0RemovedFirstLine.tif
		_7_Compressedlzw.tiff
		4RemovedFirstLine.tif
		10_Compressedlzw.tiff
		033496_437803_11.tiff
		_0_Compressedlzw.tiff
		7803_8_Compressed.png
		3RemovedFirstLine.tif
		033496_437803_13.tiff
		6033496_437803_18.jp4
		7803_4_Compressed.txt
		7803_3_Compressed.txt
		_2_Compressedlzw.tiff
		803_10_Compressed.png
		803_15_Compressed.txt
		5RemovedFirstLine.tif
		7803_7_Compressed.png
		_8_Compressedlzw.tiff
		803_13_Compressed.txt
		7803_9_Compressed.png
		033496_437803_15.tiff
		9RemovedFirstLine.tif
		803_13_Compressed.png
		6033496_437803_19.jp4
		7803_1_Compressed.txt
		7803_2_Compressed.txt
		7803_5_Compressed.txt
		8RemovedFirstLine.tif
		4RemovedFirstLine.tif
		803_12_Compressed.txt
		033496_437803_12.tiff
		12_Compressedlzw.tiff
		803_11_Compressed.png
		6033496_437803_2.tiff
		_1_Compressedlzw.tiff
		803_12_Compressed.png
		803_14_Compressed.txt
		7803_0_Compressed.png
		_3_Compressedlzw.tiff
		6033496_437803_17.jp4
		7RemovedFirstLine.tif
		7803_7_Compressed.txt
		_9_Compressedlzw.tiff
		6033496_437803_1.tiff
		2RemovedFirstLine.tif
		1RemovedFirstLine.tif
		7803_4_Compressed.png
		7803_2_Compressed.png
		3RemovedFirstLine.tif
		11_Compressedlzw.tiff
		033496_437803_14.tiff
		7803_0_Compressed.txt
		6033496_437803_16.jp4
		6033496_437803_4.tiff
		5RemovedFirstLine.tif
		6033496_437803_8.tiff
		1RemovedFirstLine.tif
		6033496_437803_9.tiff
		033496_437803_10.tiff
		803_11_Compressed.txt
		0RemovedFirstLine.tif
		_4_Compressedlzw.tiff
		7803_9_Compressed.txt
		803_15_Compressed.png
		6033496_437803_3.tiff
		803_10_Compressed.txt
		6033496_437803_7.tiff
		14_Compressedlzw.tiff
		6033496_437803_5.tiff
		15_Compressedlzw.tiff
		6033496_437803_0.tiff
		963_13_Compressed.png
		11_Compressedlzw.tiff
		7RemovedFirstLine.tif
		2RemovedFirstLine.tif
		032610_393963_11.tiff
		_1_Compressedlzw.tiff
		1RemovedFirstLine.tif
		032610_393963_12.tiff
		_7_Compressedlzw.tiff
		3963_4_Compressed.txt
		3963_4_Compressed.png
		3963_5_Compressed.txt
		3963_1_Compressed.txt
		5RemovedFirstLine.tif
		6032610_393963_0.tiff
		_3_Compressedlzw.tiff
		3RemovedFirstLine.tif
		3963_7_Compressed.txt
		1RemovedFirstLine.tif
		3963_8_Compressed.txt
		963_14_Compressed.png
		13_Compressedlzw.tiff
		6032610_393963_8.tiff
		3963_9_Compressed.png
		963_15_Compressed.png
		4RemovedFirstLine.tif
		3963_2_Compressed.png
		10_Compressedlzw.tiff
		963_12_Compressed.png
		_2_Compressedlzw.tiff
		3963_7_Compressed.png
		963_10_Compressed.png
		963_15_Compressed.txt
		3963_0_Compressed.txt
		3/NoInterference.tiff
		9RemovedFirstLine.tif
		6032610_393963_9.tiff
		14_Compressedlzw.tiff
		963_13_Compressed.txt
		_4_Compressedlzw.tiff
		963_14_Compressed.txt
		032610_393963_13.tiff
		3963_5_Compressed.png
		2RemovedFirstLine.tif
		963_11_Compressed.txt
		3963_1_Compressed.png
		_0_Compressedlzw.tiff
		4RemovedFirstLine.tif
		032610_393963_15.tiff
		3963_9_Compressed.txt
		963_10_Compressed.txt
		6032610_393963_2.tiff
		5RemovedFirstLine.tif
		6032610_393963_3.tiff
		963_11_Compressed.png
		3963_2_Compressed.txt
		3963_8_Compressed.png
		3963_3_Compressed.txt
		_9_Compressedlzw.tiff
		12_Compressedlzw.tiff
		_8_Compressedlzw.tiff
		3963_3_Compressed.png
		6032610_393963_7.tiff
		032610_393963_14.tiff
		963_12_Compressed.txt
		0RemovedFirstLine.tif
		eRemovedFirstLine.tif
		0RemovedFirstLine.tif
		6032610_393963_5.tiff
		6032610_393963_4.tiff
		032610_393963_10.tiff
		8RemovedFirstLine.tif
		_5_Compressedlzw.tiff
		3RemovedFirstLine.tif
		6032610_393963_1.tiff
		15_Compressedlzw.tiff
		3963_0_Compressed.png
		477_11_Compressed.png
		_0_Compressedlzw.tiff
		6477_1_Compressed.png
		0843156_796477_1.tiff
		0843156_796477_2.tiff
		6477_2_Compressed.txt
		0843156_796477_8.tiff
		13_Compressedlzw.tiff
		3RemovedFirstLine.tif
		3RemovedFirstLine.tif
		4RemovedFirstLine.tif
		0843156_796477_7.tiff
		0843156_796477_4.tiff
		_8_Compressedlzw.tiff
		_2_Compressedlzw.tiff
		6477_4_Compressed.png
		6477_9_Compressed.txt
		477_10_Compressed.png
		7RemovedFirstLine.tif
		477_12_Compressed.txt
		6477_2_Compressed.png
		11_Compressedlzw.tiff
		4RemovedFirstLine.tif
		1RemovedFirstLine.tif
		843156_796477_12.tiff
		6477_8_Compressed.png
		8RemovedFirstLine.tif
		14_Compressedlzw.tiff
		5RemovedFirstLine.tif
		843156_796477_13.tiff
		477_14_Compressed.png
		6477_7_Compressed.png
		12_Compressedlzw.tiff
		_7_Compressedlzw.tiff
		_9_Compressedlzw.tiff
		_1_Compressedlzw.tiff
		477_15_Compressed.txt
		0843156_796477_3.tiff
		843156_796477_11.tiff
		2RemovedFirstLine.tif
		843156_796477_10.tiff
		0843156_796477_5.tiff
		2RemovedFirstLine.tif
		6477_8_Compressed.txt
		1RemovedFirstLine.tif
		0843156_796477_9.tiff
		0RemovedFirstLine.tif
		843156_796477_14.tiff
		477_13_Compressed.png
		_4_Compressedlzw.tiff
		6477_3_Compressed.txt
		5RemovedFirstLine.tif
		477_15_Compressed.png
		6477_5_Compressed.png
		843156_796477_15.tiff
		477_11_Compressed.txt
		6477_9_Compressed.png
		_5_Compressedlzw.tiff
		6477_0_Compressed.txt
		6477_0_Compressed.png
		477_12_Compressed.png
		0RemovedFirstLine.tif
		10_Compressedlzw.tiff
		477_10_Compressed.txt
		477_13_Compressed.txt
		477_14_Compressed.txt
		6477_3_Compressed.png
		15_Compressedlzw.tiff
		_3_Compressedlzw.tiff
		6477_4_Compressed.txt
		6477_7_Compressed.txt
		9RemovedFirstLine.tif
		0843156_796477_0.tiff
		6477_5_Compressed.txt
		6477_1_Compressed.txt
		083_14_Compressed.png
		083_10_Compressed.txt
		083_9._Compressed.txt
		5RemovedFirstLine.tif
		6033067_752083_7.tiff
		_8_Compressedlzw.tiff
		_7_Compressedlzw.tiff
		8RemovedFirstLine.tif
		083_11_Compressed.txt
		033067_752083_10.tiff
		11_Compressedlzw.tiff
		6033067_752083_3.tiff
		14_Compressedlzw.tiff
		3RemovedFirstLine.tif
		2083_2_Compressed.txt
		7RemovedFirstLine.tif
		3RemovedFirstLine.tif
		1RemovedFirstLine.tif
		083_14_Compressed.txt
		13_Compressedlzw.tiff
		033067_752083_14.tiff
		2083_4_Compressed.txt
		2083_7_Compressed.txt
		83_14._Compressed.txt
		_5_Compressedlzw.tiff
		83_12._Compressed.txt
		0RemovedFirstLine.tif
		6033067_752083_19.jp4
		4RemovedFirstLine.tif
		2RemovedFirstLine.tif
		83_10._Compressed.txt
		083_4._Compressed.txt
		83_11._Compressed.txt
		083_7._Compressed.txt
		2083_0_Compressed.txt
		083_1._Compressed.txt
		12_Compressedlzw.tiff
		6033067_752083_16.jp4
		033067_752083_12.tiff
		2083_2_Compressed.png
		_9_Compressedlzw.tiff
		083_15_Compressed.txt
		083_13_Compressed.png
		2083_3_Compressed.txt
		083_12_Compressed.png
		10_Compressedlzw.tiff
		083_13_Compressed.txt
		2083_5_Compressed.txt
		2083_1_Compressed.txt
		2083_0_Compressed.png
		15_Compressedlzw.tiff
		2083_8_Compressed.png
		4RemovedFirstLine.tif
		2083_3_Compressed.png
		6033067_752083_1.tiff
		2083_9_Compressed.txt
		2083_5_Compressed.png
		_2_Compressedlzw.tiff
		083_8._Compressed.txt
		083_2._Compressed.txt
		6033067_752083_5.tiff
		2083_9_Compressed.png
		83_13._Compressed.txt
		6033067_752083_17.jp4
		_4_Compressedlzw.tiff
		033067_752083_15.tiff
		_3_Compressedlzw.tiff
		083_0._Compressed.txt
		083_3._Compressed.txt
		2083_8_Compressed.txt
		2RemovedFirstLine.tif
		9RemovedFirstLine.tif
		0RemovedFirstLine.tif
		6033067_752083_2.tiff
		6033067_752083_4.tiff
		033067_752083_13.tiff
		83_15._Compressed.txt
		083_12_Compressed.txt
		6033067_752083_8.tiff
		6033067_752083_0.tiff
		2083_1_Compressed.png
		6033067_752083_9.tiff
		033067_752083_11.tiff
		083_10_Compressed.png
		2083_4_Compressed.png
		083_11_Compressed.png
		1RemovedFirstLine.tif
		6033067_752083_18.jp4
		083_15_Compressed.png
		2083_7_Compressed.png
		5RemovedFirstLine.tif
		083_5._Compressed.txt
		_0_Compressedlzw.tiff
		_1_Compressedlzw.tiff
		773_11_Compressed.txt
		9773_8_Compressed.png
		033289_579773_11.tiff
		13_Compressedlzw.tiff
		73_13._Compressed.txt
		6033289_579773_8.tiff
		773_1._Compressed.txt
		4RemovedFirstLine.tif
		773_11_Compressed.png
		6033289_579773_2.tiff
		73_10._Compressed.txt
		_5_Compressedlzw.tiff
		033289_579773_10.tiff
		773_15_Compressed.txt
		9773_7_Compressed.png
		73_12._Compressed.txt
		773_4._Compressed.txt
		6033289_579773_3.tiff
		773_2._Compressed.txt
		6033289_579773_7.tiff
		6033289_579773_9.tiff
		_0_Compressedlzw.tiff
		14_Compressedlzw.tiff
		_1_Compressedlzw.tiff
		_4_Compressedlzw.tiff
		5RemovedFirstLine.tif
		4RemovedFirstLine.tif
		5RemovedFirstLine.tif
		1RemovedFirstLine.tif
		9773_5_Compressed.png
		_3_Compressedlzw.tiff
		773_8._Compressed.txt
		033289_579773_15.tiff
		773_13_Compressed.txt
		773_12_Compressed.txt
		9773_8_Compressed.txt
		9773_0_Compressed.txt
		15_Compressedlzw.tiff
		_9_Compressedlzw.tiff
		6033289_579773_5.tiff
		773_14_Compressed.txt
		3RemovedFirstLine.tif
		9RemovedFirstLine.tif
		773_9._Compressed.txt
		10_Compressedlzw.tiff
		73_11._Compressed.txt
		9773_4_Compressed.png
		2RemovedFirstLine.tif
		033289_579773_12.tiff
		12_Compressedlzw.tiff
		0RemovedFirstLine.tif
		2RemovedFirstLine.tif
		033289_579773_13.tiff
		9773_9_Compressed.png
		033289_579773_14.tiff
		773_12_Compressed.png
		773_15_Compressed.png
		9773_2_Compressed.txt
		11_Compressedlzw.tiff
		6033289_579773_0.tiff
		9773_9_Compressed.txt
		_2_Compressedlzw.tiff
		773_3._Compressed.txt
		0RemovedFirstLine.tif
		773_10_Compressed.png
		8RemovedFirstLine.tif
		773_14_Compressed.png
		9773_7_Compressed.txt
		7RemovedFirstLine.tif
		9773_3_Compressed.txt
		1RemovedFirstLine.tif
		3RemovedFirstLine.tif
		_7_Compressedlzw.tiff
		773_5._Compressed.txt
		6033289_579773_1.tiff
		773_10_Compressed.txt
		9773_0_Compressed.png
		9773_1_Compressed.txt
		6033289_579773_4.tiff
		9773_1_Compressed.png
		73_14._Compressed.txt
		9773_4_Compressed.txt
		773_0._Compressed.txt
		773_7._Compressed.txt
		9773_2_Compressed.png
		9773_3_Compressed.png
		773_13_Compressed.png
		73_15._Compressed.txt
		9773_5_Compressed.txt
		_8_Compressedlzw.tiff
		12_Compressedlzw.tiff
		0RemovedFirstLine.tif
		0843156_829817_3.tiff
		_8_Compressedlzw.tiff
		817_10_Compressed.png
		9817_9_Compressed.png
		817_14_Compressed.txt
		9817_3_Compressed.png
		9817_2_Compressed.png
		15_Compressedlzw.tiff
		817_11_Compressed.txt
		0843156_829817_5.tiff
		4RemovedFirstLine.tif
		2RemovedFirstLine.tif
		1RemovedFirstLine.tif
		817_15_Compressed.txt
		11_Compressedlzw.tiff
		9817_2_Compressed.txt
		9817_9_Compressed.txt
		10_Compressedlzw.tiff
		0843156_829817_0.tiff
		9817_4_Compressed.png
		1RemovedFirstLine.tif
		8RemovedFirstLine.tif
		0843156_829817_7.tiff
		_1_Compressedlzw.tiff
		_2_Compressedlzw.tiff
		_3_Compressedlzw.tiff
		843156_829817_10.tiff
		817_12_Compressed.txt
		7RemovedFirstLine.tif
		9817_8_Compressed.txt
		3RemovedFirstLine.tif
		9817_0_Compressed.png
		843156_829817_15.tiff
		13_Compressedlzw.tiff
		9817_8_Compressed.png
		5RemovedFirstLine.tif
		9817_1_Compressed.png
		0RemovedFirstLine.tif
		4RemovedFirstLine.tif
		817_12_Compressed.png
		843156_829817_12.tiff
		817_10_Compressed.txt
		5RemovedFirstLine.tif
		_5_Compressedlzw.tiff
		0843156_829817_1.tiff
		0843156_829817_2.tiff
		3RemovedFirstLine.tif
		817_11_Compressed.png
		0843156_829817_4.tiff
		_4_Compressedlzw.tiff
		9RemovedFirstLine.tif
		_7_Compressedlzw.tiff
		817_13_Compressed.txt
		0843156_829817_8.tiff
		2RemovedFirstLine.tif
		9817_3_Compressed.txt
		_9_Compressedlzw.tiff
		9817_7_Compressed.png
		9817_7_Compressed.txt
		9817_4_Compressed.txt
		843156_829817_13.tiff
		9817_1_Compressed.txt
		9817_5_Compressed.txt
		843156_829817_11.tiff
		9817_0_Compressed.txt
		817_13_Compressed.png
		0843156_829817_9.tiff
		_0_Compressedlzw.tiff
		817_14_Compressed.png
		817_15_Compressed.png
		9817_5_Compressed.png
		0843156_829817_16.jp4
		843156_829817_14.tiff
		14_Compressedlzw.tiff
		147_12_Compressed.png
		3147_9_Compressed.png
		3147_8_Compressed.txt
		843156_813147_12.tiff
		147_13_Compressed.png
		3147_1_Compressed.png
		0843156_813147_0.tiff
		0843156_813147_9.tiff
		147_12_Compressed.txt
		3147_8_Compressed.png
		2RemovedFirstLine.tif
		3147_3_Compressed.png
		843156_813147_11.tiff
		15_Compressedlzw.tiff
		3147_2_Compressed.png
		3RemovedFirstLine.tif
		9RemovedFirstLine.tif
		3147_3_Compressed.txt
		4RemovedFirstLine.tif
		1RemovedFirstLine.tif
		_8_Compressedlzw.tiff
		3RemovedFirstLine.tif
		3147_4_Compressed.png
		14_Compressedlzw.tiff
		147_14_Compressed.txt
		3147_2_Compressed.txt
		10_Compressedlzw.tiff
		5RemovedFirstLine.tif
		_7_Compressedlzw.tiff
		1RemovedFirstLine.tif
		3147_9_Compressed.txt
		2RemovedFirstLine.tif
		3147_0_Compressed.png
		3147_4_Compressed.txt
		147_10_Compressed.png
		147_15_Compressed.txt
		147_10_Compressed.txt
		7RemovedFirstLine.tif
		0843156_813147_5.tiff
		843156_813147_13.tiff
		0843156_813147_1.tiff
		0RemovedFirstLine.tif
		3147_5_Compressed.txt
		_0_Compressedlzw.tiff
		0843156_813147_4.tiff
		3147_5_Compressed.png
		8RemovedFirstLine.tif
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		_8_Compressedlzw.tiff
		293_15_Compressed.png
		11_Compressedlzw.tiff
		293_0._Compressed.txt
		7RemovedFirstLine.tif
		93_10._Compressed.txt
		6293_1_Compressed.txt
		3RemovedFirstLine.tif
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		6032738_736293_9.tiff
		2RemovedFirstLine.tif
		10_Compressedlzw.tiff
		032738_736293_15.tiff
		293_3._Compressed.txt
		_4_Compressedlzw.tiff
		6032738_736293_2.tiff
		293_13_Compressed.png
		_3_Compressedlzw.tiff
		93_13._Compressed.txt
		293_2._Compressed.txt
		4RemovedFirstLine.tif
		6032738_736293_3.tiff
		6293_5_Compressed.png
		93_11._Compressed.txt
		1RemovedFirstLine.tif
		6032738_736293_1.tiff
		6293_2_Compressed.txt
		_7_Compressedlzw.tiff
		1RemovedFirstLine.tif
		293_5._Compressed.txt
		15_Compressedlzw.tiff
		293_14_Compressed.txt
		293_4._Compressed.txt
		5RemovedFirstLine.tif
		43_10._Compressed.txt
		1RemovedFirstLine.tif
		543_7._Compressed.txt
		9543_3_Compressed.png
		_0_Compressedlzw.tiff
		_9_Compressedlzw.tiff
		543_13_Compressed.png
		543_15_Compressed.txt
		1RemovedFirstLine.tif
		_5_Compressedlzw.tiff
		6032871_679543_1.tiff
		12_Compressedlzw.tiff
		6032871_679543_5.tiff
		6032871_679543_4.tiff
		7RemovedFirstLine.tif
		43_14._Compressed.txt
		032871_679543_15.tiff
		543_8._Compressed.txt
		543_9._Compressed.txt
		543_1._Compressed.txt
		543_11_Compressed.png
		5RemovedFirstLine.tif
		4RemovedFirstLine.tif
		543_10_Compressed.png
		9543_0_Compressed.png
		9543_9_Compressed.txt
		9543_4_Compressed.png
		543_0._Compressed.txt
		9543_1_Compressed.txt
		9543_1_Compressed.png
		543_4._Compressed.txt
		9543_0_Compressed.txt
		543_10_Compressed.txt
		9543_2_Compressed.png
		3RemovedFirstLine.tif
		2RemovedFirstLine.tif
		_1_Compressedlzw.tiff
		3RemovedFirstLine.tif
		11_Compressedlzw.tiff
		6032871_679543_2.tiff
		032871_679543_12.tiff
		_4_Compressedlzw.tiff
		9543_5_Compressed.png
		43_12._Compressed.txt
		10_Compressedlzw.tiff
		9543_2_Compressed.txt
		9543_5_Compressed.txt
		9543_4_Compressed.txt
		9543_8_Compressed.txt
		9RemovedFirstLine.tif
		6032871_679543_9.tiff
		032871_679543_10.tiff
		543_13_Compressed.txt
		_2_Compressedlzw.tiff
		6032871_679543_3.tiff
		5RemovedFirstLine.tif
		0RemovedFirstLine.tif
		13_Compressedlzw.tiff
		4RemovedFirstLine.tif
		2RemovedFirstLine.tif
		43_15._Compressed.txt
		543_3._Compressed.txt
		543_15_Compressed.png
		032871_679543_13.tiff
		9543_7_Compressed.txt
		14_Compressedlzw.tiff
		9543_9_Compressed.png
		9543_8_Compressed.png
		9543_3_Compressed.txt
		0RemovedFirstLine.tif
		43_11._Compressed.txt
		543_14_Compressed.png
		_3_Compressedlzw.tiff
		9543_7_Compressed.png
		15_Compressedlzw.tiff
		543_12_Compressed.png
		_8_Compressedlzw.tiff
		6032871_679543_7.tiff
		543_12_Compressed.txt
		543_5._Compressed.txt
		6032871_679543_8.tiff
		543_11_Compressed.txt
		543_14_Compressed.txt
		8RemovedFirstLine.tif
		032871_679543_11.tiff
		43_13._Compressed.txt
		6032871_679543_0.tiff
		_7_Compressedlzw.tiff
		543_2._Compressed.txt
		032871_679543_14.tiff
		3137_8_Compressed.png
		137_10_Compressed.txt
		1RemovedFirstLine.tif
		9RemovedFirstLine.tif
		137_12_Compressed.txt
		3137_5_Compressed.txt
		_3_Compressedlzw.tiff
		0843156_763137_8.tiff
		15_Compressedlzw.tiff
		0843156_763137_5.tiff
		843156_763137_10.tiff
		3137_5_Compressed.png
		3137_4_Compressed.png
		3137_1_Compressed.png
		137_13_Compressed.png
		12_Compressedlzw.tiff
		_1_Compressedlzw.tiff
		3137_3_Compressed.txt
		0RemovedFirstLine.tif
		843156_763137_14.tiff
		3137_0_Compressed.png
		3137_4_Compressed.txt
		13_Compressedlzw.tiff
		3137_7_Compressed.png
		137_13_Compressed.txt
		1RemovedFirstLine.tif
		0843156_763137_2.tiff
		_2_Compressedlzw.tiff
		4RemovedFirstLine.tif
		3RemovedFirstLine.tif
		137_14_Compressed.png
		843156_763137_11.tiff
		0843156_763137_7.tiff
		2RemovedFirstLine.tif
		137_15_Compressed.png
		0843156_763137_0.tiff
		3137_9_Compressed.png
		0843156_763137_3.tiff
		_4_Compressedlzw.tiff
		7RemovedFirstLine.tif
		3137_2_Compressed.png
		137_15_Compressed.txt
		_8_Compressedlzw.tiff
		3137_1_Compressed.txt
		2RemovedFirstLine.tif
		_7_Compressedlzw.tiff
		137_10_Compressed.png
		0843156_763137_1.tiff
		11_Compressedlzw.tiff
		5RemovedFirstLine.tif
		137_14_Compressed.txt
		0843156_763137_4.tiff
		8RemovedFirstLine.tif
		3137_2_Compressed.txt
		_5_Compressedlzw.tiff
		137_12_Compressed.png
		_9_Compressedlzw.tiff
		843156_763137_12.tiff
		3137_8_Compressed.txt
		10_Compressedlzw.tiff
		0RemovedFirstLine.tif
		3137_9_Compressed.txt
		5RemovedFirstLine.tif
		_0_Compressedlzw.tiff
		3137_7_Compressed.txt
		14_Compressedlzw.tiff
		4RemovedFirstLine.tif
		137_11_Compressed.png
		3137_3_Compressed.png
		3137_0_Compressed.txt
		0843156_763137_9.tiff
		3RemovedFirstLine.tif
		843156_763137_13.tiff
		843156_763137_15.tiff
		137_11_Compressed.txt
		843156_746467_10.tiff
		2RemovedFirstLine.tif
		6467_8_Compressed.txt
		6467_8_Compressed.png
		843156_746467_13.tiff
		843156_746467_11.tiff
		11_Compressedlzw.tiff
		9RemovedFirstLine.tif
		_2_Compressedlzw.tiff
		467_14_Compressed.txt
		467_11_Compressed.txt
		843156_746467_15.tiff
		467_10_Compressed.txt
		6467_2_Compressed.txt
		6467_4_Compressed.png
		0843156_746467_9.tiff
		6467_1_Compressed.txt
		1RemovedFirstLine.tif
		6467_2_Compressed.png
		6467_9_Compressed.png
		1RemovedFirstLine.tif
		467_15_Compressed.txt
		0843156_746467_2.tiff
		0843156_746467_3.tiff
		6467_5_Compressed.png
		10_Compressedlzw.tiff
		6467_7_Compressed.png
		3RemovedFirstLine.tif
		0843156_746467_4.tiff
		6467_3_Compressed.png
		7RemovedFirstLine.tif
		13_Compressedlzw.tiff
		467_15_Compressed.png
		4RemovedFirstLine.tif
		5RemovedFirstLine.tif
		5RemovedFirstLine.tif
		467_14_Compressed.png
		0RemovedFirstLine.tif
		15_Compressedlzw.tiff
		467_12_Compressed.png
		467_13_Compressed.png
		0RemovedFirstLine.tif
		_8_Compressedlzw.tiff
		6467_4_Compressed.txt
		0843156_746467_7.tiff
		6467_9_Compressed.txt
		6467_7_Compressed.txt
		_0_Compressedlzw.tiff
		0843156_746467_18.jp4
		6467_1_Compressed.png
		2RemovedFirstLine.tif
		843156_746467_14.tiff
		_1_Compressedlzw.tiff
		843156_746467_12.tiff
		6467_3_Compressed.txt
		_3_Compressedlzw.tiff
		0843156_746467_1.tiff
		467_10_Compressed.png
		3RemovedFirstLine.tif
		467_12_Compressed.txt
		467_13_Compressed.txt
		_7_Compressedlzw.tiff
		14_Compressedlzw.tiff
		4RemovedFirstLine.tif
		0843156_746467_19.jp4
		0843156_746467_8.tiff
		_9_Compressedlzw.tiff
		8RemovedFirstLine.tif
		0843156_746467_0.tiff
		6467_0_Compressed.png
		6467_0_Compressed.txt
		0843156_746467_5.tiff
		_5_Compressedlzw.tiff
		12_Compressedlzw.tiff
		467_11_Compressed.png
		_4_Compressedlzw.tiff
		6467_5_Compressed.txt
		1442

		%% Cell type:code id: tags:

		``` python
		```

Remove_Noise.py

+47 −32

Original line number	Diff line number	Diff line
		@@ -100,15 +100,26 @@ def find_only_in_channel(images, channel_name = "10"):
		same_sensor_images.append(image_name)
		return same_sensor_images
		def adjust_to_original(new_image, average_image):
		# original_image_min = np.min(new_image)
		# original_image_max = np.max(new_image)
		average_image = average_image - np.mean(average_image)
		adjusted_image = new_image - average_image
		# adjusted_image = new_image + (average_image - gaussian_filter(average_image,sigma=5))
		original_image_min = np.min(new_image)
		original_image_max = np.max(new_image)
		# average_image = average_image - np.mean(average_image)
		# adjusted_image = average_image - new_image
		# adjusted_image = gaussian_filter(new_image,sigma=1)

		adjusted_image = new_image - (average_image - gaussian_filter(average_image,sigma=1))
		# adjusted_image = gaussian_filter(adjusted_image,sigma=20)
		# adjusted_image = new_image + (average_image - np.array(Image.fromarray(average_image).convert("L").filter(ImageFilter.GaussianBlur(radius=4))))
		# adjusted_image = adjusted_image - np.min(adjusted_image)
		# adjusted_image = adjusted_image*(original_image_max-original_image_min)/np.max(adjusted_image)
		# adjusted_image = adjusted_image + original_image_min
		plt.subplot(121)
		plt.imshow(color_adjust((adjusted_image)),cmap='gray',vmin = 0, vmax=1)
		plt.subplot(122)
		plt.imshow(color_adjust(new_image),cmap='gray',vmin = 0, vmax=1)
		plt.show()


		adjusted_image = adjusted_image - np.min(adjusted_image)
		adjusted_image = adjusted_image*(original_image_max-original_image_min)/np.max(adjusted_image)
		adjusted_image = adjusted_image + original_image_min
		print(adjusted_image.dtype)
		return adjusted_image.astype(np.uint16)

		def color_adjust(visual_array):
		@@ -121,8 +132,8 @@ def save_new_average(quantity_of_images = 1500, channel = "10", head_dir = "/med
		scenes = remote_file_extractor(head_dir)
		images = find_only_in_channel(remote_image_extractor(scenes),channel)
		if quantity_of_images != "all":
		# images = np.random.choice(images,quantity_of_images,replace = False)
		images = images[:quantity_of_images]
		images = np.random.choice(images,quantity_of_images,replace = False)
		# images = images[:quantity_of_images]
		average_image = remote_create_average(images,channel)
		# average_image = average_image.astype(int)
		average_savable_image = Image.fromarray(average_image)
		@@ -132,25 +143,25 @@ def create_testable_images(images, selected_channel, quantity_of_images):
		sftp_client = setup_remote_sftpclient()
		images = find_only_in_channel(images, selected_channel)

		image_locations = np.random.choice(len(images), quantity_of_images, replace=False)
		# image_locations = np.arange(quantity_of_images) + 10000
		# image_locations = np.random.choice(len(images), quantity_of_images, replace=False)
		image_locations = np.arange(quantity_of_images) + 10000

		selected_images = np.array(images)[image_locations]

		# average_image = np.array(Image.open("Average_On_Channel(" + selected_channel + ").tiff"))
		images_in_each_direction = 40
		average_image = np.array(Image.open("Average_On_Channel(" + selected_channel + ").tiff"))
		images_in_each_direction = 80
		for i, item in enumerate(selected_images):
		if image_locations[i] < images_in_each_direction:
		average_image = remote_create_average(images[image_locations[i] - image_locations[i]: image_locations[i] + images_in_each_direction + image_locations[i]], selected_channel)
		elif image_locations[i] > (len(images) - images_in_each_direction):
		average_image = remote_create_average(images[image_locations[i] - images_in_each_direction - (len(images) - image_locations[i]): image_locations[i] + (len(images) - image_locations[i])], selected_channel)
		else:
		average_image = remote_create_average(images[image_locations[i] - images_in_each_direction: image_locations[i] + images_in_each_direction], selected_channel)
		# if image_locations[i] < images_in_each_direction:
		# average_image = remote_create_average(images[image_locations[i] - image_locations[i]: image_locations[i] + images_in_each_direction + image_locations[i]], selected_channel)
		# elif image_locations[i] > (len(images) - images_in_each_direction):
		# average_image = remote_create_average(images[image_locations[i] - images_in_each_direction - (len(images) - image_locations[i]): image_locations[i] + (len(images) - image_locations[i])], selected_channel)
		# else:
		# average_image = remote_create_average(images[image_locations[i] - images_in_each_direction: image_locations[i] + images_in_each_direction], selected_channel)
		image = Image.open(sftp_client.open(item))
		wherelastslash = item.rfind("/")
		image = np.array(image)[1:]
		savable_original = Image.fromarray(image)
		savable_original.save("averaged_images(" + selected_channel + ")/innerfolder/original" + item[wherelastslash + 1:])
		# savable_original.save("averaged_images(" + selected_channel + ")/innerfolder/original" + item[wherelastslash + 1:])
		altered_image = adjust_to_original(image, average_image)
		altered_image = Image.fromarray(altered_image)

		@@ -160,19 +171,19 @@ def create_testable_images(images, selected_channel, quantity_of_images):
		sftp_client.close()

		if __name__ == "__main__":
		# save_new_average(15,"11")
		# save_new_average(350,"11")
		scenes = remote_file_extractor("/media/elphel/NVME/lwir16-proc/te0607/scenes/")
		images = remote_image_extractor(scenes)
		images = find_only_in_channel(images, "11")
		# average_image = np.array(Image.open("Average_On_Channel(" + "11" + ").tiff"))
		create_testable_images(images,"11",2)
		create_testable_images(images,"11",3)
		# plt.imshow(color_adjust(average_image),cmap='gray',vmin = 0, vmax=1)
		# plt.show()

		# print(len(images))
		average_image = remote_create_average(images[10000 - 10: 10000 + 10], "11")
		plt.imshow(color_adjust((average_image - gaussian_filter(average_image,sigma=5))),cmap='gray',vmin = 0, vmax=1)
		plt.show()
		# plt.imshow(color_adjust((average_image - gaussian_filter(average_image,sigma=5))),cmap='gray',vmin = 0, vmax=1)
		# plt.show()
		sftp_client = setup_remote_sftpclient()
		print(len(images))
		# print(images[10000])
		@@ -185,11 +196,15 @@ if __name__ == "__main__":
		# newimage = Image.fromarray(test_image - average_image)
		# newimage.save("NoInterference.tiff")

		plt.subplot(121)
		plt.imshow(color_adjust(test_image),cmap='gray',vmin = 0, vmax=1)
		plt.subplot(122)
		plt.imshow(color_adjust(adjust_to_original(test_image,average_image)),cmap='gray',vmin = 0, vmax=1)
		plt.show()
		# plt.subplot(121)
		# plt.imshow(color_adjust(test_image),cmap='gray',vmin = 0, vmax=1)
		# plt.subplot(122)
		# plt.imshow(color_adjust(adjust_to_original(test_image,average_image)),cmap='gray',vmin = 0, vmax=1)
		# plt.show()
		sftp_client.close()
		# print(np.linalg.inv(np.array([[3,0,-1],[0,3,3],[1,-3,-4]])))
		# print(np.linalg.pinv(np.array([[-1,-1,1], [-1,0,1], [-1,1,1], [0,-1,1]])))

		last_image = Image.open("NoInterference.tiff")
		# plt.imshow(color_adjust(np.array(last_image)),cmap='gray',vmin = 0, vmax=1)
		# plt.show()
		No newline at end of file

VideoToImage.ipynb

0 → 100644

+53 −0

Original line number	Diff line number	Diff line
		%% Cell type:code id: tags:

		``` python
		import cv2
		vidcap = cv2.VideoCapture("concat_mono-fg_realtime.mp4")
		success,image = vidcap.read()
		count = 0
		while success and count < 5:
		cv2.imwrite("betterimages/innerfolder/fram%d.jpg" % count, image, 0)
		success, image = vidcap.read()
		count += 1
		```

		%% Output

		---------------------------------------------------------------------------
		SystemError Traceback (most recent call last)
		/home/bryce/git/master/VideoToImage.ipynb Cell 1' in <cell line: 5>()
		<a href='vscode-notebook-cell:/home/bryce/git/master/VideoToImage.ipynb#ch0000000?line=3'>4</a> count = 0
		<a href='vscode-notebook-cell:/home/bryce/git/master/VideoToImage.ipynb#ch0000000?line=4'>5</a> while success and count < 5:
		----> <a href='vscode-notebook-cell:/home/bryce/git/master/VideoToImage.ipynb#ch0000000?line=5'>6</a> cv2.imwrite("betterimages/innerfolder/fram%d.jpg" % count, image, 0)
		<a href='vscode-notebook-cell:/home/bryce/git/master/VideoToImage.ipynb#ch0000000?line=6'>7</a> success, image = vidcap.read()
		<a href='vscode-notebook-cell:/home/bryce/git/master/VideoToImage.ipynb#ch0000000?line=7'>8</a> count += 1
		SystemError: <built-in function imwrite> returned NULL without setting an error

		%% Cell type:code id: tags:

		``` python
		from PIL import Image
		import numpy as np
		for i in range(5):
		im = Image.open("betterimages/innerfolder/fram" + str(i) + ".jpg", )
		print(np.array(im).shape)
		im.save("betterimages/innerfolder/fram" + str(i) + ".tiff", 'TIFF')
		```

		%% Output

		(512, 640, 3)
		(512, 640, 3)
		(512, 640, 3)
		(512, 640, 3)
		(512, 640, 3)

		%% Cell type:code id: tags:

		``` python
		```

		%% Cell type:code id: tags:

		``` python
		```

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