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Tiff file format for pre-processed quad-stereo sets

Fri, 07/13/2018 - 14:13

‎TIFF stacks for ML

← Older revision Revision as of 20:13, 13 July 2018 (2 intermediate revisions by the same user not shown)Line 45: Line 45: ==TIFF stacks for ML== ==TIFF stacks for ML== −[[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]]+[[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]] [[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]] Line 54: Line 54: *** '''hor-pairs''' *** '''hor-pairs''' *** '''vert-pairs''' *** '''vert-pairs''' −*** '''other''' - encoded values: estimated disparity, residual disparity and confidence for the residual disparity+*** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * There are a few ways to view the stack: * There are a few ways to view the stack: Oleg

Tiff file format for pre-processed quad-stereo sets

Fri, 07/13/2018 - 13:19

File:Ml tiff stack imagej.jpeg

Fri, 07/13/2018 - 13:17

Oleg uploaded a new version of File:Ml tiff stack imagej.jpeg

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== Licensing ==
{{CC }} Oleg

Tiff file format for pre-processed quad-stereo sets

Thu, 07/12/2018 - 18:49

‎Python

← Older revision Revision as of 00:49, 13 July 2018 (One intermediate revision by the same user not shown)Line 110: Line 110: values data: (242, 324, 3) values data: (242, 324, 3) − +[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing (actually, see the CVPR2018 presentation, p.23)]] '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: * '''Pack image tiles for better structuring for ML''' * '''Pack image tiles for better structuring for ML''' Oleg

Tiff file format for pre-processed quad-stereo sets

Thu, 07/12/2018 - 14:20

‎Python

← Older revision Revision as of 20:20, 12 July 2018 Line 110: Line 110: values data: (242, 324, 3) values data: (242, 324, 3) − +[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing]] '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: * '''Pack image tiles for better structuring for ML''' * '''Pack image tiles for better structuring for ML''' Oleg

File:Ml tiff stack python tile packing.jpeg

Thu, 07/12/2018 - 14:20

Oleg uploaded File:Ml tiff stack python tile packing.jpeg

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== Licensing ==
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File:Ml tiff stack python values.jpeg

Thu, 07/12/2018 - 14:13

Oleg uploaded a new version of File:Ml tiff stack python values.jpeg

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== Licensing ==
{{CC }} Oleg

Tiff file format for pre-processed quad-stereo sets

Thu, 07/12/2018 - 14:08

← Older revision Revision as of 20:08, 12 July 2018 (4 intermediate revisions by the same user not shown)Line 47: Line 47: [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] +[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]] * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] Line 59: Line 60: ImageJ - it has a native support for stacks, each stack has a name label stored (along with related xml info) in the ImageJ tiff tags. To read tiff tags in ImageJ, go '''Image > Show Info...''' ImageJ - it has a native support for stacks, each stack has a name label stored (along with related xml info) in the ImageJ tiff tags. To read tiff tags in ImageJ, go '''Image > Show Info...''' ====Python==== ====Python==== −Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:+'''1.''' Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: * '''Get tiff tags values (Pillow)''' * '''Get tiff tags values (Pillow)''' * '''Parse Properties xml data stored by ImageJ in the tiff tags''' * '''Parse Properties xml data stored by ImageJ in the tiff tags''' Line 104: Line 105: −Upon opening tiff the image shape will be '''(height,width,layer)''' - for further processing it needs to be reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example:+Upon opening tiff the image will be a numpy array of shape '''(height,width,layer)''' - for further processing it is reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example: tiff stack shape: (2178, 2916, 5) tiff stack shape: (2178, 2916, 5) image data: (242, 324, 9, 9, 4) image data: (242, 324, 9, 9, 4) values data: (242, 324, 3) values data: (242, 324, 3) + + +'''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: +* '''Pack image tiles for better structuring for ML''' + '''# The current packing is hardcoded in the script: (TY,TX,9,9,4) -> (TY,TX,100)''' + # Get tiles from a tiff stack + import pack_tile as pile + packed_tiles = pile.pack(tile) + # packed_tiles get stacked with '''estimated disparity''' (see '''test_nn_feed.py''') + packed_tiles = np.dstack((packed_tiles,values[:,:,0])) Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 17:19

← Older revision Revision as of 23:19, 11 July 2018 (One intermediate revision by the same user not shown)Line 47: Line 47: [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] +[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]] * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] Line 104: Line 105: −Upon opening tiff the image shape will be '''(height,width,layer)''' - for further processing it needs to be reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example:+Upon opening tiff the image will be a numpy array of shape '''(height,width,layer)''' - for further processing it is reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example: tiff stack shape: (2178, 2916, 5) tiff stack shape: (2178, 2916, 5) image data: (242, 324, 9, 9, 4) image data: (242, 324, 9, 9, 4) values data: (242, 324, 3) values data: (242, 324, 3) Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 16:50

‎TIFF stacks for ML

← Older revision Revision as of 22:50, 11 July 2018 Line 47: Line 47: [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] +[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]] * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] Oleg

File:Ml tiff stack python data layers.jpeg

Wed, 07/11/2018 - 16:49

Oleg uploaded File:Ml tiff stack python data layers.jpeg

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== Licensing ==
{{CC }} Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 16:44

‎Python

← Older revision Revision as of 22:44, 11 July 2018 (4 intermediate revisions by the same user not shown)Line 45: Line 45: ==TIFF stacks for ML== ==TIFF stacks for ML== +[[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] +[[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] Line 58: Line 60: ====Python==== ====Python==== Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: −* get tiff tags values (Pillow)+* '''Get tiff tags values (Pillow)''' −* parse Properties xml data stored in the tiff tags used by ImageJ+* '''Parse Properties xml data stored by ImageJ in the tiff tags''' −* get tile dimensions from Properties+* '''Get tiles dimensions from Properties''' −* read layers as numpy arrays for further computations or plotting+* '''Convert layers to numpy arrays (split into tiles or optionally not split) for further computations and plotting''' −Example:+Example (more examples are commented out in the __main__ section of the script): '''~$ python3 imagej_tiff.py 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff''' '''~$ python3 imagej_tiff.py 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff''' time: 1531344391.7055812 time: 1531344391.7055812 Oleg

File:Ml tiff stack python values.jpeg

Wed, 07/11/2018 - 16:20

Oleg uploaded File:Ml tiff stack python values.jpeg

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== Licensing ==
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File:Ml tiff stack imagej.jpeg

Wed, 07/11/2018 - 16:19

Oleg uploaded File:Ml tiff stack imagej.jpeg

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== Licensing ==
{{CC }} Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 15:48

‎TIFF stacks for ML

← Older revision Revision as of 21:48, 11 July 2018 (15 intermediate revisions by the same user not shown)Line 3: Line 3: '''1527256903_350165/''' '''1527256903_350165/''' ├── 1527256903_350165.kml ├── 1527256903_350165.kml − ├── '''jp4'''+ ├── '''jp4''' (source files directory) │ ├── 1527256903_350165_0.jp4 │ ├── 1527256903_350165_0.jp4 │ ├── ... │ ├── ... Line 12: Line 12: ├── rating.txt ├── rating.txt ├── thumb.jpeg ├── thumb.jpeg − └── '''v03'''+ └── '''v03''' (model version) ├── 1527256903_350165-00-D0.0.jpeg ├── 1527256903_350165-00-D0.0.jpeg ├── ... ├── ... Line 26: Line 26: ├── 1527256903_350165.obj ├── 1527256903_350165.obj ├── 1527256903_350165.x3d ├── 1527256903_350165.x3d − └── '''ml'''+ └── '''ml''' (directory with processed data files for ML) ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff Line 34: Line 34: where: where: * '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system. * '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system. −* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a common polynom+* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a distortion polynom common for each image * '''*.corr-xml''' - ImageJ plugin's settings file? * '''*.corr-xml''' - ImageJ plugin's settings file? * '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack * '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack Line 40: Line 40: * '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model * '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model * '''*.obj, *.mtl, *.png''' - OBJ format model with textures * '''*.obj, *.mtl, *.png''' - OBJ format model with textures −* '''ml/*.tiff''' - TIFF stack of pre-processed images for ML+* '''*.tiff''' - TIFF stack of pre-processed images for ML * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only −==Stacked TIFF==+==TIFF stacks for ML== − +* What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: +** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] +*** '''diagm-pair''' +*** '''diago-pair''' +*** '''hor-pairs''' +*** '''vert-pairs''' +*** '''other''' - encoded values: estimated disparity, residual disparity and confidence for the residual disparity * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * There are a few ways to view the stack: * There are a few ways to view the stack: −** just open with ImageJ+====ImageJ==== +ImageJ - it has a native support for stacks, each stack has a name label stored (along with related xml info) in the ImageJ tiff tags. To read tiff tags in ImageJ, go '''Image > Show Info...''' +====Python==== +Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: +* get tiff tags values (Pillow) +* parse Properties xml data stored in the tiff tags used by ImageJ +* get tile dimensions from Properties +* read layers as numpy arrays for further computations or plotting +Example: + '''~$ python3 imagej_tiff.py 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff''' + time: 1531344391.7055812 + time: 1531344392.5336654 + TIFF stack labels: ['diagm-pair', 'diago-pair', 'hor-pairs', 'vert-pairs', 'other'] + <?xml version="1.0" ?> + <properties> + <ML_OTHER_TARGET>0</ML_OTHER_TARGET> + <tileWidth>9</tileWidth> + <disparityRadiusMain>257.22231560274076</disparityRadiusMain> + <comment_ML_OTHER_GTRUTH_STRENGTH>Offset of the ground truth strength in the "other" layer tile</comment_ML_OTHER_GTRUTH_STRENGTH> + <data_min>-0.16894744988183344</data_min> + <comment_intercameraBaseline>Horizontal distance between the main and the auxiliary camera centers (mm). Disparity is specified for the main camera</comment_intercameraBaseline> + <ML_OTHER_GTRUTH>2</ML_OTHER_GTRUTH> + <data_max>0.6260986600450271</data_max> + <disparityRadiusAux>151.5308819757923</disparityRadiusAux> + <comment_disparityRadiusAux>Side of the square where 4 main camera subcameras are located (mm). Disparity is specified for the main camera</comment_disparityRadiusAux> + <comment_disparityRadiusMain>Side of the square where 4 main camera subcameras are located (mm)</comment_disparityRadiusMain> + <comment_dispOffset>Tile target disparity minum ground truth disparity</comment_dispOffset> + <comment_tileWidth>Square tile size for each 2d correlation, always odd</comment_tileWidth> + <comment_data_min>Defined only for 8bpp mode - value, corresponding to -127 (-128 is NaN)</comment_data_min> + <comment_data_max>Defined only for 8bpp mode - value, corresponding to +127 (-128 is NaN)</comment_data_max> + <comment_ML_OTHER_TARGET>Offset of the target disparity in the "other" layer tile</comment_ML_OTHER_TARGET> + <VERSION>1.0</VERSION> + <dispOffset>0.0</dispOffset> + <comment_ML_OTHER_GTRUTH>Offset of the ground truth disparity in the "other" layer tile</comment_ML_OTHER_GTRUTH> + <ML_OTHER_GTRUTH_STRENGTH>4</ML_OTHER_GTRUTH_STRENGTH> + <intercameraBaseline>1256.0</intercameraBaseline> + </properties> + Tiles shape: 9x9 + Data min: -0.16894744988183344 + Data max: 0.6260986600450271 + (2178, 2916, 5) + Stack of images shape: (242, 324, 9, 9, 4) + time: 1531344392.7290232 + Stack of values shape: (242, 324, 3) + time: 1531344393.5556033 + + + +Upon opening tiff the image shape will be '''(height,width,layer)''' - for further processing it needs to be reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example: + tiff stack shape: (2178, 2916, 5) + image data: (242, 324, 9, 9, 4) + values data: (242, 324, 3) Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 14:42

‎TIFF stacks for ML

← Older revision Revision as of 20:42, 11 July 2018 (12 intermediate revisions by the same user not shown)Line 3: Line 3: '''1527256903_350165/''' '''1527256903_350165/''' ├── 1527256903_350165.kml ├── 1527256903_350165.kml − ├── '''jp4'''+ ├── '''jp4''' (source files directory) │ ├── 1527256903_350165_0.jp4 │ ├── 1527256903_350165_0.jp4 │ ├── ... │ ├── ... Line 12: Line 12: ├── rating.txt ├── rating.txt ├── thumb.jpeg ├── thumb.jpeg − └── '''v03'''+ └── '''v03''' (model version) ├── 1527256903_350165-00-D0.0.jpeg ├── 1527256903_350165-00-D0.0.jpeg ├── ... ├── ... Line 26: Line 26: ├── 1527256903_350165.obj ├── 1527256903_350165.obj ├── 1527256903_350165.x3d ├── 1527256903_350165.x3d − └── '''ml'''+ └── '''ml''' (directory with processed data files for ML) ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff Line 34: Line 34: where: where: * '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system. * '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system. −* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a common polynom+* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a distortion polynom common for each image * '''*.corr-xml''' - ImageJ plugin's settings file? * '''*.corr-xml''' - ImageJ plugin's settings file? * '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack * '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack Line 40: Line 40: * '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model * '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model * '''*.obj, *.mtl, *.png''' - OBJ format model with textures * '''*.obj, *.mtl, *.png''' - OBJ format model with textures −* '''ml/*.tiff''' - TIFF stack of pre-processed images for ML+* '''*.tiff''' - TIFF stack of pre-processed images for ML * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only −==Stacked TIFF==+==TIFF stacks for ML== − +* What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: +** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] +*** '''diagm-pair''' +*** '''diago-pair''' +*** '''hor-pairs''' +*** '''vert-pairs''' +*** '''other''' - encoded values: image disparity, estimated disparity and confidence for the estimated disparity * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * There are a few ways to view the stack: * There are a few ways to view the stack: −** just open with ImageJ+** Open with ImageJ - it has a native support for stacks, each stack has a name label stored (along with related xml info) in the ImageJ tiff tags. To read tiff tags in ImageJ, go '''Image > Show Info...''' +** Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] +*** Upon opening tiff the image shape will be '''(height,width,layer)''' - for further processing it needs to be reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''': + tiff stack shape: (2178, 2916, 5) + image data: (242, 324, 9, 9, 4) + values data: (242, 324, 3) Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 13:39

← Older revision Revision as of 19:39, 11 July 2018 (4 intermediate revisions by the same user not shown)Line 3: Line 3: '''1527256903_350165/''' '''1527256903_350165/''' ├── 1527256903_350165.kml ├── 1527256903_350165.kml − ├── '''jp4'''+ ├── '''jp4''' (source files directory) │ ├── 1527256903_350165_0.jp4 │ ├── 1527256903_350165_0.jp4 │ ├── ... │ ├── ... Line 12: Line 12: ├── rating.txt ├── rating.txt ├── thumb.jpeg ├── thumb.jpeg − └── '''v03'''+ └── '''v03''' (model version) ├── 1527256903_350165-00-D0.0.jpeg ├── 1527256903_350165-00-D0.0.jpeg ├── ... ├── ... Line 26: Line 26: ├── 1527256903_350165.obj ├── 1527256903_350165.obj ├── 1527256903_350165.x3d ├── 1527256903_350165.x3d − └── '''ml'''+ └── '''ml''' (directory with processed data files for ML) ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff ├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff Line 34: Line 34: where: where: * '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system. * '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system. −* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a common polynom+* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a distortion polynom common for each image * '''*.corr-xml''' - ImageJ plugin's settings file? * '''*.corr-xml''' - ImageJ plugin's settings file? * '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack * '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack Line 40: Line 40: * '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model * '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model * '''*.obj, *.mtl, *.png''' - OBJ format model with textures * '''*.obj, *.mtl, *.png''' - OBJ format model with textures −* '''ml/*.tiff''' - TIFF stack of pre-processed images for ML+* '''*.tiff''' - TIFF stack of pre-processed images for ML * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only −==Stacked TIFF==+==TIFF stacks for ML== * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * There are a few ways to view the stack: * There are a few ways to view the stack: ** just open with ImageJ ** just open with ImageJ Oleg

Tiff file format for pre-processed quad-stereo sets

Wed, 07/11/2018 - 13:08

Created page with "==Image sets== Example tree of a single set: '''1527256903_350165/''' ├── 1527256903_350165.kml ├── '''jp4''' │ ├── <font color='Royal..."

New page

==Image sets==
Example tree of a single set:
'''1527256903_350165/'''
├── 1527256903_350165.kml
├── '''jp4'''
│ ├── 1527256903_350165_0.jp4
│ ├── ...
│ ├── 1527256903_350165_3.jp4
│ ├── 1527256903_350165_4.jp4
│ ├── ...
│ └── 1527256903_350165_7.jp4
├── rating.txt
├── thumb.jpeg
└── '''v03'''
├── 1527256903_350165-00-D0.0.jpeg
├── ...
├── 1527256903_350165-07-D0.0.jpeg
├── 1527256903_350165.corr-xml
├── 1527256903_350165-DSI_COMBO.tiff
├── 1527256903_350165-EXTRINSICS.corr-xml
├── 1527256903_350165-img1-texture.png
├── ...
├── 1527256903_350165-img2001-texture.png
├── 1527256903_350165-img_infinity-texture.png
├── 1527256903_350165.mtl
├── 1527256903_350165.obj
├── 1527256903_350165.x3d
└── '''ml'''
├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-2.00000.tiff
├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS-1.00000.tiff
├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff
├── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS1.00000.tiff
└── 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS2.00000.tiff
where:
* '''*.jp4''' - source files, 0..3 - quad stereo camera #1, 4..7 - quad stereo camera #2, and so on if there are more cameras in the system.
* '''*-D0.0.jpeg''' - disparity = 0, images are undistorted to a common polynom
* '''*.corr-xml''' - ImageJ plugin's settings file?
* '''*-DSI_COMBO.tiff''' - Disparity Space Image - tiff stack
* '''*-EXTRINSICS.corr-xml''' - extrinsic parameters of the multicamera system
* '''*.x3d, *.png''' - X3D format model with textures. The textures are shared with the OBJ format model
* '''*.obj, *.mtl, *.png''' - OBJ format model with textures
* '''ml/*.tiff''' - TIFF stack of pre-processed images for ML

* *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only

==Stacked TIFF==

* The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack
* There are a few ways to view the stack:
** just open with ImageJ Oleg

Tensorflow with gpu

Fri, 07/06/2018 - 11:07

‎Setup (some details)

← Older revision Revision as of 17:07, 6 July 2018 Line 49: Line 49: # Export paths # Export paths ~$ export PATH=/usr/local/cuda-9.2/bin${PATH:+:${PATH}} ~$ export PATH=/usr/local/cuda-9.2/bin${PATH:+:${PATH}} − ~$ export LD_LIBRARY_PATH=/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}+ ~$ export LD_LIBRARY_PATH=/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} + ~$ export LD_LIBRARY_PATH=/usr/local/cuda-9.2/extras/CUPTI/lib64/${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}} * Install TensorFlow (build from sources for cuda 9.2): * Install TensorFlow (build from sources for cuda 9.2): Oleg

Poky manual

Tue, 06/26/2018 - 12:25

‎Setup

← Older revision Revision as of 18:25, 26 June 2018 Line 85: Line 85: bitbake u-boot device-tree linux-xlnx core-image-elphel393 bitbake u-boot device-tree linux-xlnx core-image-elphel393 −* Poky 2.2 Jethro+* Poky 2.0 Jethro − git clone https://git.elphel.com/Elphel/elphel393.git # or git clone git@git.elphel.com:Elphel/elphel393.git # if ssh public key is uploaded+ git clone -b jethro https://git.elphel.com/Elphel/elphel393.git # or git clone git@git.elphel.com:Elphel/elphel393.git # if ssh public key is uploaded # then follow the same steps as for Rocko # then follow the same steps as for Rocko Oleg

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Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

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Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

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Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

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Tiff file format for pre-processed quad-stereo sets

File:Ml tiff stack python values.jpeg

File:Ml tiff stack imagej.jpeg

Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

Tiff file format for pre-processed quad-stereo sets

Tensorflow with gpu

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