| 99 | | * '''Coordinate aspect ratio:''' when '''[!CheckFixAspectRatio]''' is selected (the default option for images), the scale ratio for the x and y coordinates is fixed to 1 by default (it can be manually adjusted by the edit box '''[num_AspectRatio]'''. When '''[ |
| 100 | | |
| 101 | | * '''Extracting graphs:''' The graph displayed in the central window can be copied to a separate figure by pressing the menu bar command '''[Export/extract figure]'''. This allows plot editing, exporting in image format and printing, using standard Matlab graphic tools. Plots can be also exported on an existing figure for data comparison, using the option '''[Export/export on axis]'''. A movie can be produced using the command [Export/make movie avi]. |
| 102 | | |
| 103 | | * '''Extracting data''' as Matlab arrays. Information stored in the GUI uvmat (as 'UserData' in the figure) can be extracted in the Matlab work space by the menu bar command '''[Export/field in workspace]''' (or by pressing the right mouse button on the GUI). Type '>>Data_uvmat.Field' to get the current input field as a Matlab structure. An image or scalar matrix is for instance obtained as Data_uvmat.Field.A. |
| | 99 | * '''Coordinate aspect ratio:''' when '''[!CheckFixAspectRatio]''' is selected (the default option for images), the scale ratio for the x and y coordinates is fixed to 1 by default (it can be manually adjusted by the edit box '''[num_AspectRatio]'''. When '''[!CheckFixAspectRatio]''' is not selected the graph scales along x and y automatically adjust to the figure size. |
| | 100 | |
| | 101 | * '''Extracting graphs:''' The graph displayed in the central window can be copied to a separate figure by pressing the menu bar command '''[Export/extract figure]'''. This allows plot editing, exporting in image format and printing, using standard Matlab graphic tools. Plots can be also exported on an existing figure for data comparison, using the option '''[Export/export on axis]'''. A movie can be produced using the command '''[Export/make movie avi]'''. |
| | 102 | |
| | 103 | * '''Extracting data''' as Matlab arrays. Information stored in the GUI uvmat (as ''!UserData'' in the figure) can be extracted in the Matlab work space by the menu bar command '''[Export/field in workspace]''' (or by pressing the right mouse button on the GUI). Type '>>Data_uvmat.Field' to get the current input field as a Matlab structure. An image or scalar matrix is for instance obtained as Data_uvmat.Field.A. |
| 108 | | uvmat can read any image format recognised by the Matlab image reading function ({imread.m}. Images can be in true color or B&W, with 8 bit or 16 bit grey levels. Image files containing multiple frames are handled. Movie files can be also opened, using the Matlab function {VideoReader.m}, or {mmreader.m} for older versions of Matlab. |
| 109 | | |
| 110 | | Velocity fields and all results of data processing are stored in the Netcdf format, see [section 7->#get_field] for details. They are read by the function {nc2struct.m} . Then different quantities (vorticity, divergence...) can be calculated by the function {calc_scal.m}. |
| 111 | | |
| 112 | | The PIV software CIVx requires B&W images in the format png (portable network graphics). It is a binary format for images with lossless (reversible) compression, recommended by w3c ([->http://www.w3.org/Graphics/PNG] ). It is an open source patent-free replacement of GIF and can also replace many common uses of TIFF. It can be read directly by all standard programs of image visualisation and processing. Compressing a raw binary image to its c png form typically saves disk storage by a factor of 3. |
| | 108 | uvmat can read any image format recognised by the Matlab image reading function ''imread.m''. Images can be in true color or B&W, with 8 bit or 16 bit grey levels. Image files containing multiple frames are handled. Movie files can be also opened, using the Matlab function ''!VideoReader.m'', or ''mmreader.m'' for older versions of Matlab. |
| | 109 | |
| | 110 | Velocity fields and all results of data processing are stored in the Netcdf format, see [wiki:#a7Netcdffilesandget_field.fig: section 7-] for details. They are read by the function ''nc2struct.m''. Then different quantities (vorticity, divergence...) can be obtained. |
| | 111 | |
| | 112 | The PIV software CIVx requires B&W images in the format png (portable network graphics). It is a binary format for images with lossless (reversible) compression, recommended by w3c (http://www.w3.org/Graphics/PNG). It is an open source patent-free replacement of GIF and can also replace many common uses of TIFF. It can be read directly by all standard programs of image visualisation and processing. Compressing a raw binary image to its png form typically saves disk storage by a factor of 3. |
| 117 | | The uvmat package recognizes the NetCDF fields obtained from the CIVx software. This includes the velocity fields and their spatial derivatives, as well as information about the CIV processing (image correlation values and flags). The vorticity, divergence, or strain are read in the same NetCDF files, but are available only after a PATCH operation has been run in the CIVx software, see [section 10->#civ]. |
| | 117 | The package uvmat recognizes the NetCDF fields obtained from the CIVx software. This includes the velocity fields and their spatial derivatives, as well as information about the CIV processing (image correlation values and flags). The vorticity, divergence, or strain are read in the same NetCDF files, but are available only after a PATCH operation has been run in the CIVx software, see [#a11-PIV:ParticleImagingVelocimetrys: section 11]. |
| 128 | | Different kinds of file or image frame indexing are defined: |
| 129 | | |
| 130 | | -'''Simple series:''' files in a series can be labeled by a single integer index i, with name obtained by concatenation of the full root ({RootPath/RootFile}), an index string suffix, and the file extension {FileExt} (example {Exp01/aa_45.png}). A frame series can be alternatively read from a singlemovie file. Then the index i stands for the frame index within the file. |
| | 128 | Different kinds of file or image frame indexing are defined: |
| | 129 | |
| | 130 | -'''Simple series:''' files in a series can be labeled by a single integer index i, with name obtained by concatenation of the full root ''!RootPath/RootFile''), an index string suffix, and the file extension ''!FileExt'' (example ''Exp01/aa_45.png''). A frame series can be alternatively read from a single movie file. Then the index ''i'' stands for the frame index within the file. |
| 136 | | -'''Nomenclature types:''' These different indexing systems are implemented by a functions {fullfile_uvmat.m}. The inputs are the root name, four indices i1,i2,j1,j2 and a character string representing the nomenclature type. The reverse operation, splitting a name into a root and indices while detecting the nomenclature type, is performed by the function {fileparts_uvmat.m}. Once the nomenclature type has been detected by the browser of '''uvmat.fig''', it is displayed in the edit box '''[NomType]''' of u'''vmat.fig'''. This nomenclature type is defined as the index string for the first file in the series, for instance '_1' for a single indexing and '1_1-2' for a double indexing. For a field series in a single file, like a movie, the nomenclature type is '*'. For a set of indexed movies (or multimage files), the index i labels the files while the index j labels the frames within a file. |
| | 136 | -'''Nomenclature types:''' These different indexing systems are implemented by a functions {fullfile_uvmat.m}. The inputs are the root name, four indices i1,i2,j1,j2 and a character string representing the nomenclature type. The reverse operation, splitting a name into a root and indices while detecting the nomenclature type, is performed by the function {fileparts_uvmat.m}. Once the nomenclature type has been detected by the browser of '''uvmat.fig''', it is displayed in the edit box '''[!NomType]''' of '''uvmat.fig'''. This nomenclature type is defined as the index string for the first file in the series, for instance '_1' for a single indexing and '1_1-2' for a double indexing. For a field series in a single file, like a movie, the nomenclature type is '*'. For a set of indexed movies (or multimage files), the index i labels the files while the index j labels the frames within a file. |
| 143 | | The current indices are displayed in the four edit boxes '''[i1], [i2], [j1], [j2]'''. The two first indices i1 and j1 are used for image series, while the second line i2, j2 is used to label the image pairs used for PIV data. The file indices can be directly set in these edit boxes, or equivalently in the edit box '''[FileIndex]''' at the top of the GUI. |
| 144 | | |
| 145 | | For navigation with index pairs, the reference index, defined as the integer part of the mean value ((j1+j2)/2), is incremented. If the check box '''[fix_pair] ''' is selected, the difference j1-j2 is then fixed while the reference index i or j is incremented. Else the pair with appropriate reference index is searched. In the case of multiple choices, the most largest index interval is chosen. This allows us to scan successive fields obtained with different image pairs (to deal with time evolving velocity fields). |
| | 143 | The current indices are displayed in the four edit boxes '''[i1], [i2], [j1], [j2]'''. The two first indices i1 and j1 are used for image series, while the second line i2, j2 is used to label the image pairs used for PIV data. The file indices can be directly set in these edit boxes, or equivalently in the edit box '''[!FileIndex]''' at the top of the GUI. |
| | 144 | |
| | 145 | For navigation with index pairs, the reference index, defined as the integer part of the mean value ((j1+j2)/2), is incremented. If the check box '''[fix_pair] ''' is selected, the difference j1-j2 is then fixed while the reference index i or j is incremented. Else the pair with appropriate reference index is searched. In the case of multiple choices, the most largest index interval is chosen. This allows us to scan successive fields obtained with different image pairs (to deal with time evolving velocity fields). |
| 156 | | Information on image series is provided by a documentation file in the format xml. This file can include sections about image timing, geometric calibration, camera type and illumination. An xml file is a text file in which each element of information, or group of elements, is labelled by a tag. The list of tags and their hierarchical organisation is specified by a schema file (.xsd). The schema used for image documentation is {ImaDoc.xsd}, available in the uvmat package at the path indicated in {PARAM.xml}). For a general introduction to the xml language, see [http://www.w3schools.com/xml->http://www.w3schools.com/xml]. |
| 157 | | |
| 158 | | When a new file series is opened in uvmat, a documentation file is automatically sought, whose path and name are displayed by {RootPath} and {RootFile} respectively, with extension {.xml} ({RootPath} and {RootFile} are the contents of the edit boxes '''[RootPath]''' and ''' [RootFile]'''). The detection of this file is indicated by the visibility of the pushbutton '''[view_xml]''' on the upper right of the GUI '''uvmat.fig'''. Press this button to see the content through an xml editor '''editxml.fig''' (described in [section 9 ->#series]). The xml file can be also opened directly by the uvmat browser, or by any text editor. |
| 159 | | |
| 160 | | The xml file <code><ImaDoc> </code> can contain the following sections: |
| | 156 | Information on image series is provided by a documentation file in the format xml. This file can include sections about image timing, geometric calibration, camera type and illumination. An xml file is a text file in which each element of information, or group of elements, is labelled by a tag. The list of tags and their hierarchical organisation is specified by a schema file (.xsd). The schema used for image documentation is ''ImaDoc.xsd'', available in the uvmat package at the path indicated in {PARAM.xml}). For a general introduction to the xml language, see http://www.w3schools.com/xml. |
| | 157 | |
| | 158 | When a new file series is opened in uvmat, a documentation file is automatically sought, whose path and name are displayed by ''!RootPath'' and ''!RootFile'' respectively, with extension {.xml} (''!RootPath'' and ''!RootFile'' are the contents of the edit boxes '''[!RootPath]''' and ''' [!RootFile]'''). The detection of this file is indicated by the visibility of the pushbutton '''[view_xml]''' on the upper right of the GUI '''uvmat.fig'''. Press this button to see the content through an xml editor '''editxml.fig''' (described in [wiki:#a10-Processingfieldseries: section 10]). The xml file can be also opened directly by the uvmat browser, or by any text editor. |
| | 159 | |
| | 160 | The xml file <code><ImaDoc> </code> can contain the following sections: |
| 391 | | NetCDF (network Common Data Form) is a machine-independent format for representing scientific data, suitable for large arrays ([->http://www.unidata.ucar.edu/software/netcdf/]). Each piece of data can be directly accessed by its name without reading the whole file. New records can be added to the file without perturbing the remaining information. The next release of NetCDF is intended to be compatible with the newly developed and more general hdf format. |
| 392 | | |
| 393 | | The NetCDF format has been initially developed for meteorological data, but has been progressively chosen by many scientific communities. This format has been for instance proposed by the European network PIVNet ( http://www.meol.cnrs.fr/LML/EuroPIV2/Proceedings/p251.pdf ) to inter compare data obtained by various techniques of Particle Imaging Velocimetry. |
| 394 | | |
| 395 | | Libraries for reading-writing and data visualisation with usual computer languages can be freely downloaded. Recent releases of Matlab contain built in functions for reading and writting netcdf files. For old versions, a free toolbox must be downloaded from from http://sourceforge.net/projects/mexcdf/. Uvmat deals with both cases. |
| | 391 | NetCDF (network Common Data Form) is a machine-independent format for representing scientific data, suitable for large arrays (http://www.unidata.ucar.edu/software/netcdf/). Each piece of data can be directly accessed by its name without reading the whole file. New records can be added to the file without perturbing the remaining information. The next release of NetCDF is intended to be compatible with the newly developed and more general hdf format. |
| | 392 | |
| | 393 | The NetCDF format has been initially developed for meteorological data, but has been progressively chosen by many scientific communities. This format has been for instance proposed by the European network PIVNet (http://www.meol.cnrs.fr/LML/EuroPIV2/Proceedings/p251.pdf ) to inter compare data obtained by various techniques of Particle Imaging Velocimetry. |
| | 394 | |
| | 395 | Libraries for reading-writing and data visualisation with usual computer languages can be freely downloaded. Recent releases of Matlab contain built in functions for reading and writting netcdf files. For old versions, a free toolbox must be downloaded from from http://sourceforge.net/projects/mexcdf/. Uvmat deals with both cases. |
