restructure data, generated metadata for niis

code/extract_metadata/p.py

@@ -0,0 +1,37 @@
+import nibabel as nib
+
+from os import path
+from os.path import isdir
+import os
+import numpy as np
+import json
+
+def read_metadata(path_to_nii=None):
+  nii=nib.load(path_to_nii)
+  data=nii.get_fdata()
+  max=np.max(data)
+  min=np.min(data)
+  return {
+    'max': max,
+    'min': min
+  }
+
+file_path = path.dirname(path.abspath(__file__))
+root_dir=path.join(file_path, '../..')
+
+path_to_nii=path.join(root_dir, 'output/data')
+path_to_metadata=path.join(root_dir, 'output/metadata')
+
+dirs=os.listdir(path_to_nii)
+
+for dir in dirs:
+  print(f'processing {dir}')
+
+  os.makedirs(path.join(path_to_metadata, dir), exist_ok=True)
+
+  files=os.listdir(path.join(path_to_nii, dir))
+  for file in files:
+    path_to_map=path.join(path_to_nii, dir, file)
+    metadata=read_metadata(path_to_map)
+    with open(path.join(path_to_metadata, dir, f'{file}.json'), 'w', encoding='utf-8') as fp:
+      json.dump(metadata, fp, indent=2, ensure_ascii=False)

code/split_niftis/err.log

@@ -0,0 +1,24 @@
+Traceback (most recent call last):
+  File "p.py", line 34, in <module>
+    data=nii.dataobj[..., chan_idx:chan_idx+1]
+  File "/home/xiao/dev/datalad/difumo/scripts/venv/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 397, in __getitem__
+    return self._get_scaled(dtype=None, slicer=slicer)
+  File "/home/xiao/dev/datalad/difumo/scripts/venv/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 358, in _get_scaled
+    scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
+  File "/home/xiao/dev/datalad/difumo/scripts/venv/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 345, in _get_unscaled
+    lock=self._lock)
+  File "/home/xiao/dev/datalad/difumo/scripts/venv/lib/python3.6/site-packages/nibabel/fileslice.py", line 790, in fileslice
+    arr_data = read_segments(fileobj, segments, n_bytes, lock)
+  File "/home/xiao/dev/datalad/difumo/scripts/venv/lib/python3.6/site-packages/nibabel/fileslice.py", line 678, in read_segments
+    fileobj.seek(offset)
+  File "/home/xiao/dev/datalad/difumo/scripts/venv/lib/python3.6/site-packages/nibabel/openers.py", line 166, in seek
+    return self.fobj.seek(*args, **kwargs)
+  File "/usr/lib/python3.6/gzip.py", line 368, in seek
+    return self._buffer.seek(offset, whence)
+  File "/usr/lib/python3.6/_compression.py", line 143, in seek
+    data = self.read(min(io.DEFAULT_BUFFER_SIZE, offset))
+  File "/usr/lib/python3.6/gzip.py", line 485, in read
+    self._add_read_data( uncompress )
+  File "/usr/lib/python3.6/gzip.py", line 490, in _add_read_data
+    self._crc = zlib.crc32(data, self._crc)
+KeyboardInterrupt

code/split_niftis/out.log

@@ -0,0 +1,6 @@
+processing 1024
+finished processing 0
+finished processing 10
+finished processing 20
+finished processing 30
+finished processing 40

code/split_niftis/p.py

@@ -0,0 +1,40 @@
+import nibabel as nib
+from os import path
+from os.path import isdir
+import os
+import numpy as np
+
+def convert_nii(path_to_nii=None):
+  nii=nib.load(path_to_nii)
+  data=nii.get_fdata()
+  shape=data.shape
+  print(shape)
+
+file_path = path.dirname(path.abspath(__file__))
+root_dir=path.join(file_path, '../..')
+
+path_to_input=path.join(root_dir, 'input')
+dirs=os.listdir(path_to_input)
+
+for dir in dirs:
+  print(f'processing {dir}')
+
+  os.makedirs(path.join(root_dir, f'output/{dir}'), exist_ok=True)
+  path_to_map=path.join(path_to_input, dir, 'maps.nii.gz')
+
+  num_chan=int(dir)
+  
+  nii=nib.load(path_to_map)
+  nii_hdr=nii.header
+  nii_hdr.set_xyzt_units('mm', 'sec')
+  nii_affine=nii.affine
+
+  chan_idx=0
+  while chan_idx < num_chan:
+    data=nii.dataobj[..., chan_idx:chan_idx+1]
+
+    img=nib.Nifti1Image(data,header=nii_hdr,affine=nii_affine)
+    nib.save(img, path.join(root_dir, f'output/{dir}/{str(chan_idx + 1)}.nii.gz'))
+    if chan_idx % 10 == 0:
+      print(f'finished processing {chan_idx}')
+    chan_idx += 1

code/split_niftis/s.sh

@@ -0,0 +1,7 @@
+#! /bin/bash
+
+for f in $(find . -name '*.nii.gz'); do
+strip_prefix=${f#./};
+num_name=${strip_prefix%.nii.gz}
+echo $num_name;
+done

code/split_niftis/tmp.py

@@ -0,0 +1,11 @@
+import nibabel as nib
+nii=nib.load('../input/64/maps.nii.gz')
+nii_hdr=nii.header
+nii_affine=nii.affine
+
+data=nii.dataobj[..., 0:1]
+
+nii_hdr.set_xyzt_units('mm', 'sec')
+img=nib.Nifti1Image(data,header=nii_hdr,affine=nii_affine)
+
+nib.save(img, './t.nii.gz')

output/1024/0.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/mG/68/MD5E-s27128--af79f573329c326ab74db37bc3c9248c.nii.gz/MD5E-s27128--af79f573329c326ab74db37bc3c9248c.nii.gz

output/1024/1.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/J5/zq/MD5E-s27708--da2648d47618d87446b102607d054bc1.nii.gz/MD5E-s27708--da2648d47618d87446b102607d054bc1.nii.gz

output/1024/10.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/kQ/X8/MD5E-s27127--f38cead2e34c2f3302148a857f9d46f9.nii.gz/MD5E-s27127--f38cead2e34c2f3302148a857f9d46f9.nii.gz

output/1024/100.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/m6/kp/MD5E-s26893--f8938956bf40486c86769ddc9626eeef.nii.gz/MD5E-s26893--f8938956bf40486c86769ddc9626eeef.nii.gz

output/1024/1000.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/67/Jq/MD5E-s27493--ad08b238a32a4fc0a7bbe73d12961ccf.nii.gz/MD5E-s27493--ad08b238a32a4fc0a7bbe73d12961ccf.nii.gz

output/1024/1001.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/V4/44/MD5E-s27758--767ed57d7d09c3c9e44a2336ac941ac8.nii.gz/MD5E-s27758--767ed57d7d09c3c9e44a2336ac941ac8.nii.gz

output/1024/1002.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/FG/9m/MD5E-s27257--c32ab9efc15db9cc70640836305b6ef1.nii.gz/MD5E-s27257--c32ab9efc15db9cc70640836305b6ef1.nii.gz

output/1024/1003.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/F9/98/MD5E-s27053--04c516e8f3f032ccadddeac0ba1ac523.nii.gz/MD5E-s27053--04c516e8f3f032ccadddeac0ba1ac523.nii.gz

output/1024/1004.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/pz/gW/MD5E-s27967--4c635aaaed633fff5503d6ccbce9c3f0.nii.gz/MD5E-s27967--4c635aaaed633fff5503d6ccbce9c3f0.nii.gz

output/1024/1005.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/P4/qZ/MD5E-s27388--f04c1d5ead72a2d4d66a08acbe57f09b.nii.gz/MD5E-s27388--f04c1d5ead72a2d4d66a08acbe57f09b.nii.gz

output/1024/1006.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/1X/w2/MD5E-s27378--92657eb496af0af20d0a28996eff68f1.nii.gz/MD5E-s27378--92657eb496af0af20d0a28996eff68f1.nii.gz

output/1024/1007.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/XX/XW/MD5E-s27446--0f19f2b3bcd04c75e92759b23e2bb58c.nii.gz/MD5E-s27446--0f19f2b3bcd04c75e92759b23e2bb58c.nii.gz

output/1024/1008.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/93/1q/MD5E-s27559--c2875d531ecf0b111b021239f80cfe27.nii.gz/MD5E-s27559--c2875d531ecf0b111b021239f80cfe27.nii.gz

output/1024/1009.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/k8/mg/MD5E-s26849--f5f210dd0dd8ba4388d353d80b038b85.nii.gz/MD5E-s26849--f5f210dd0dd8ba4388d353d80b038b85.nii.gz

output/1024/101.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/1F/fK/MD5E-s27026--ec4ebcbc7ea9b32283181e315500372e.nii.gz/MD5E-s27026--ec4ebcbc7ea9b32283181e315500372e.nii.gz

output/1024/1010.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/V1/55/MD5E-s27520--c81f9b29660f42974dec4a631bfb5a44.nii.gz/MD5E-s27520--c81f9b29660f42974dec4a631bfb5a44.nii.gz

output/1024/1011.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/pv/P0/MD5E-s27760--3fd798c70ad3afa403c6bc122cffa2c9.nii.gz/MD5E-s27760--3fd798c70ad3afa403c6bc122cffa2c9.nii.gz

output/1024/1012.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/0k/40/MD5E-s26875--2ed0be798aa7719b7e801ae5d759342d.nii.gz/MD5E-s26875--2ed0be798aa7719b7e801ae5d759342d.nii.gz

output/1024/1013.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/09/3p/MD5E-s27852--ab3aaae7ab7034b3fcca975f7e3cb842.nii.gz/MD5E-s27852--ab3aaae7ab7034b3fcca975f7e3cb842.nii.gz

output/1024/1014.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/44/1V/MD5E-s26890--4341a7a3ca72eff75feaf7934c4a5465.nii.gz/MD5E-s26890--4341a7a3ca72eff75feaf7934c4a5465.nii.gz

output/1024/1015.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/KV/F3/MD5E-s27968--a3cb177bc38a2e848f5b5b0a21c92c22.nii.gz/MD5E-s27968--a3cb177bc38a2e848f5b5b0a21c92c22.nii.gz

output/1024/1016.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/XJ/VP/MD5E-s28311--e7828ad86c2712596d8f45271fd7f73f.nii.gz/MD5E-s28311--e7828ad86c2712596d8f45271fd7f73f.nii.gz

output/1024/1017.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/PG/8m/MD5E-s27692--7b365b29146045d5e080e2fe4da3ab04.nii.gz/MD5E-s27692--7b365b29146045d5e080e2fe4da3ab04.nii.gz

output/1024/1018.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/GX/PX/MD5E-s27403--a2264c4a040133ba55ef7737ccb55a45.nii.gz/MD5E-s27403--a2264c4a040133ba55ef7737ccb55a45.nii.gz

output/1024/1019.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/6G/07/MD5E-s27078--ff1703dafa4d648c4c1687bed394aaee.nii.gz/MD5E-s27078--ff1703dafa4d648c4c1687bed394aaee.nii.gz

output/1024/102.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/V6/8g/MD5E-s27078--16ec356a1ce045b97659c2c658971682.nii.gz/MD5E-s27078--16ec356a1ce045b97659c2c658971682.nii.gz

output/1024/1020.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/1f/GM/MD5E-s28151--ec2e2c5a4d75d7a39822d82cf810e729.nii.gz/MD5E-s28151--ec2e2c5a4d75d7a39822d82cf810e729.nii.gz

output/1024/1021.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/VV/5g/MD5E-s27817--e798c045fba0a723c11e3b5761d7e5a0.nii.gz/MD5E-s27817--e798c045fba0a723c11e3b5761d7e5a0.nii.gz

output/1024/1022.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/Q4/W8/MD5E-s27890--d2b43c1f1e0f0201d9868add5dd79864.nii.gz/MD5E-s27890--d2b43c1f1e0f0201d9868add5dd79864.nii.gz

output/1024/1023.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/3f/JG/MD5E-s27493--6dc5958a1ba8f0920860c944c733f8d5.nii.gz/MD5E-s27493--6dc5958a1ba8f0920860c944c733f8d5.nii.gz

output/1024/103.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/Xp/8w/MD5E-s26803--1f09211127a55d6482eaba8a4a8ce4f4.nii.gz/MD5E-s26803--1f09211127a55d6482eaba8a4a8ce4f4.nii.gz

output/1024/104.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/Kx/G8/MD5E-s27046--7af698bd00f1c7e2e7a48ecbc32852c8.nii.gz/MD5E-s27046--7af698bd00f1c7e2e7a48ecbc32852c8.nii.gz

output/1024/105.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/mg/qJ/MD5E-s27641--5adba8a0f323d26aad0c5bb03fdf9693.nii.gz/MD5E-s27641--5adba8a0f323d26aad0c5bb03fdf9693.nii.gz

output/1024/106.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/7Q/k0/MD5E-s27903--82a2bb136e9c9af8ee51e9be3fed9d32.nii.gz/MD5E-s27903--82a2bb136e9c9af8ee51e9be3fed9d32.nii.gz

output/1024/107.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/zg/wq/MD5E-s27054--fc4360f9c176a63d079672e02fd23ca4.nii.gz/MD5E-s27054--fc4360f9c176a63d079672e02fd23ca4.nii.gz

output/1024/108.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/42/VW/MD5E-s28612--3bdb6400fef3a09a467aaa3d0a9bbf9b.nii.gz/MD5E-s28612--3bdb6400fef3a09a467aaa3d0a9bbf9b.nii.gz

output/1024/109.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/vp/PX/MD5E-s26788--0f868983bb59305e712317ae45300706.nii.gz/MD5E-s26788--0f868983bb59305e712317ae45300706.nii.gz

output/1024/11.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/4q/8X/MD5E-s27294--b9394cf3b213f1953247ecc5c5c1a173.nii.gz/MD5E-s27294--b9394cf3b213f1953247ecc5c5c1a173.nii.gz

output/1024/110.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/7K/x6/MD5E-s28313--ab1b280abfaaa29f5f17825a8f346104.nii.gz/MD5E-s28313--ab1b280abfaaa29f5f17825a8f346104.nii.gz

output/1024/111.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/v4/xZ/MD5E-s27525--6a35e75fc452c3a9c24e806941a6b277.nii.gz/MD5E-s27525--6a35e75fc452c3a9c24e806941a6b277.nii.gz

output/1024/112.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/wQ/x1/MD5E-s27577--c505939103f2319202879b6ede89d74f.nii.gz/MD5E-s27577--c505939103f2319202879b6ede89d74f.nii.gz

output/1024/113.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/j7/FG/MD5E-s26886--71f92441bac2a04d9e7cd21500ce9583.nii.gz/MD5E-s26886--71f92441bac2a04d9e7cd21500ce9583.nii.gz

output/1024/114.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/gv/47/MD5E-s27586--01e4c2112ee086b0cd4c19b0cf6b8b4a.nii.gz/MD5E-s27586--01e4c2112ee086b0cd4c19b0cf6b8b4a.nii.gz

output/1024/115.nii.gz

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output/1024/116.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/pv/xG/MD5E-s26819--22949e2e2e6abc8dd848c0eed9822629.nii.gz/MD5E-s26819--22949e2e2e6abc8dd848c0eed9822629.nii.gz

output/1024/117.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/M5/wQ/MD5E-s28608--5e38ee21a2f28b34d512b3184027e11a.nii.gz/MD5E-s28608--5e38ee21a2f28b34d512b3184027e11a.nii.gz

output/1024/118.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/F1/PF/MD5E-s27593--c632b97b5b8b57709cdce6f40cdfbdd9.nii.gz/MD5E-s27593--c632b97b5b8b57709cdce6f40cdfbdd9.nii.gz

output/1024/119.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/j3/VZ/MD5E-s27162--684622d7717284982a5e2d7207ffd05f.nii.gz/MD5E-s27162--684622d7717284982a5e2d7207ffd05f.nii.gz

output/1024/12.nii.gz

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-../../.git/annex/objects/Qx/65/MD5E-s27582--709e3208904cc7bf0252cf21bbf9840e.nii.gz/MD5E-s27582--709e3208904cc7bf0252cf21bbf9840e.nii.gz

output/1024/120.nii.gz

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-../../.git/annex/objects/68/3J/MD5E-s26979--3e1ddb284ad5206836f70363dba0d3d6.nii.gz/MD5E-s26979--3e1ddb284ad5206836f70363dba0d3d6.nii.gz

output/1024/121.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/GQ/XP/MD5E-s27410--c770755e76a2d577da23944a756c3b8a.nii.gz/MD5E-s27410--c770755e76a2d577da23944a756c3b8a.nii.gz

output/1024/122.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/fm/Jw/MD5E-s27439--65e19c9ec57fea1e678c09038843f42b.nii.gz/MD5E-s27439--65e19c9ec57fea1e678c09038843f42b.nii.gz

output/1024/123.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/xW/33/MD5E-s28019--d15203642c6d8785357b3d15517fd190.nii.gz/MD5E-s28019--d15203642c6d8785357b3d15517fd190.nii.gz

output/1024/124.nii.gz

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-../../.git/annex/objects/62/M6/MD5E-s29712--b6fdc72d8468aaa30d8f176379a09d1c.nii.gz/MD5E-s29712--b6fdc72d8468aaa30d8f176379a09d1c.nii.gz

output/1024/125.nii.gz

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-../../.git/annex/objects/0p/F9/MD5E-s26729--21ec70c650307221e65566654e9394c7.nii.gz/MD5E-s26729--21ec70c650307221e65566654e9394c7.nii.gz

output/1024/126.nii.gz

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-../../.git/annex/objects/JP/WM/MD5E-s28772--a1a6aab13e9e5aa788e950851fa6c3ff.nii.gz/MD5E-s28772--a1a6aab13e9e5aa788e950851fa6c3ff.nii.gz

output/1024/127.nii.gz

@@ -1 +0,0 @@
-../../.git/annex/objects/z8/Xz/MD5E-s26989--8db083caaa6dee73b52facd51fe54b90.nii.gz/MD5E-s26989--8db083caaa6dee73b52facd51fe54b90.nii.gz

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