Class Fileserver

Takes care of all file handling to and from the image area and provides commodity functions for creating and displaying previews.

Namespace: hrm
Package: hrm
Located at Fileserver.php

Methods summary

`public`	# `__construct( string $name )` Fileserver constructor. Fileserver constructor. Parameters `$name` User name.
`public boolean`	# `isReachable( )` Checks whether the file area is reachable. Checks whether the file area is reachable. Returns boolean True if the file area is reachable (i.e. if source and destination folders exist). Todo Test if accessible/writable.
`public string`	# `username( )` Returns the name of the user. Returns the name of the user. Returns string Name of the user.
`public string`	# `sourceFolder( )` Returns the absolute path to the user's source image folder. The folder may be on the local network. Returns the absolute path to the user's source image folder. The folder may be on the local network. Returns string Absolute path to the source image folder.
`public string`	# `destinationFolder( )` Returns the absolute path to the user's destination image folder. The folder may be on the local network Returns the absolute path to the user's destination image folder. The folder may be on the local network Returns string Absolute path to the destination image folder.
`public string`	# `destinationFolderFor( hrm\job\JobDescription $desc )` Returns the destination image folder from a JobDescription object Returns the destination image folder from a JobDescription object Parameters `$desc` JobDescription object.@ Returns string Festination image folder with user-generated subfolder.
`public array\|boolean`	# `files( string $extension = null )` Searches the source folder recursively, stores and also returns the list of found files Searches the source folder recursively, stores and also returns the list of found files Parameters `$extension` Extension to be considered to scan the folder. Omit to get all files. Returns array\|boolean Sorted array of file names or false if the source folder does not exist. Todo Do not return different types!
`public string`	# `checkAgainstFormat( string $file, string $selectedFormat )` Extracts the file extension, also if it's a subimage. Extracts the file extension, also if it's a subimage. Parameters `$file` The file name. `$selectedFormat` The format selected at the select images stage. Returns string The file extension.
`public array`	# `listFiles( boolean $expand )` Searches the source folder recursively and returns all found files Searches the source folder recursively and returns all found files Parameters `$expand` If true, names of subimages (as in the case of lif files) are expanded and returned in the list of file names. Please notice that this function DOES NOT STORE THE LIST OF FILES. It just returns it! Returns array Sorted array of file names. Todo Refactor!
`public array\|boolean`	# `destFiles( string $extension = null )` Searches the destination folder recursively and returns all found files. Searches the destination folder recursively and returns all found files. Parameters `$extension` Extension to be considered to scan the folder. Omit to get all files. Returns array\|boolean Sorted array of file names or false if the destination folder does not exist. Todo Do not return different types!
`public array`	# `condenseSeries( )` Condense file series by preserving only the first file of each series. Condense file series by preserving only the first file of each series. Files that do not belong to a series are preserved. Returns array Updated (condensed) list of stored files.
`public boolean`	# `isPartOfFileSeries( string $file )` Checks whether a given file belongs to a file series. Checks whether a given file belongs to a file series. Parameters `$file` The file to be checked. Returns boolean True if the file belongs to a series, false otherwise.
`public array`	# `filesOfType( string $format, boolean $isTimeSeries )` A wrapper function to list files of a certain type. A wrapper function to list files of a certain type. This updates the list of stored files. Parameters `$format` Extension to be considered to scan the folder. `$isTimeSeries` True for time series, false otherwise. Returns array Array of of file names. Todo Refactor!
`public array`	# `allFiles( )` Scans the image source folder recursively and returns all files. Scans the image source folder recursively and returns all files. This does not update the stored list! Returns array Sorted array of file names
`public array`	# `tiffFiles( )` Convenience method to get TIFF files. Convenience method to get TIFF files. This stores the files. Returns array Array of TIFF file names.
`public array`	# `tiffSeriesFiles( )` Convenience method to get numbered TIFF series. Convenience method to get numbered TIFF series. This stores the files. Returns array Array of numbered TIFF file names.
`public array`	# `tiffLeicaFiles( )` Convenience method to get TIFF series with Leica style numbering Convenience method to get TIFF series with Leica style numbering This stores the files. Returns array Array of Leica TIFF file names.
`public array`	# `stkFiles( )` Convenience method to get all STK files (also unprocessed time series). Convenience method to get all STK files (also unprocessed time series). This stores the files. Returns array Array of STK files with unprocessed time series.
`public array`	# `stkSeriesFiles( )` Convenience method to get STK time series files (_t#.stk). Convenience method to get STK time series files (_t#.stk). This stores the files. Returns array Array of STK time series files.
`public`	# `resetFiles( )` Resets the list of source files. Next time the list is accessed it will be recreated automatically. Resets the list of source files. Next time the list is accessed it will be recreated automatically.
`public`	# `resetDestFiles( )` Resets the list of destination files. Next time the list is accessed it will be recreated automatically. Resets the list of destination files. Next time the list is accessed it will be recreated automatically.
`public`	# `expandSubImages( boolean $bool )` Sets a flag to indicate whether multi-experiment image files should be expanded in file lists or not. Sets a flag to indicate whether multi-experiment image files should be expanded in file lists or not. Parameters `$bool` True if multi-image files should be expanded; false otherwise.
`public array`	# `selectedFiles( )` Returns the list of selected files that will be added to a job. Returns the list of selected files that will be added to a job. Returns array Array of selected file names.
`public`	# `addFilesToSelection( array $files )` Add files to current selection if they are not already contained. Add files to current selection if they are not already contained. Parameters `$files` Array of file names to be added.
`public`	# `removeAllFilesFromSelection( )` Remove all files from current selection. Remove all files from current selection.
`public`	# `removeFilesFromSelection( array $files )` Remove files from current selection (if they are in). Remove files from current selection (if they are in). Parameters `$files` Array of file names to be removed,
`public string`	# `getFilePattern( string $fileName )` Builds a regular expression to be able to look for files based on the job id. Builds a regular expression to be able to look for files based on the job id. Parameters `$fileName` File name to be parsed to construct the regular expression. Returns string The regular expression. Todo A new design and implementation of the file server is necessary.
`public string`	# `downloadResults( array $files )` Packs a series of files to download. Packs a series of files to download. Parameters `$files` List of files to be added. Returns string Success/error message. Todo This will be replaced soon!
`public string`	# `deleteFiles( array $files, string $dir = "dest" )` Deletes a list of files and all dependent sub-files (e.g. thumbnails and so) from a user directory. Deletes a list of files and all dependent sub-files (e.g. thumbnails and so) from a user directory. Parameters `$files` Array of image file names. `$dir` Folder to consider, one of 'src' or 'dest' Returns string Error message in case files could not be deleted.
`public`	# `exportToOmero( )` Exports a deconvolved image to the OMERO server. Exports a deconvolved image to the OMERO server.
`public`	# `importFromOmero( )` Imports a raw image from the OMERO server. Imports a raw image from the OMERO server.
`public`	# `decompressArchive( string $file, string $type, string $dest, &string & $okMsg, &string & $errMsg, string $subdir = "", boolean $imagesOnly = true )` Extracts files from compressed archives. Extracts files from compressed archives. Parameters `$file` Archive name. `$type` Archive type (zip, tar, tgz...). `$dest` Destination path. `$okMsg` A reference to a string to accumulate OK messages. `$errMsg` A reference to a string to accumulate error messages. `$subdir` An optional subdirectory under $dest to expand the files to. `$imagesOnly` An optional flag to delete non-image files after extraction.
`public string`	# `uploadFiles( array $files, string $dir )` Processes the $_FILES array posted when uploading files, moving valid one to the specified directory. Compressed files are decompressed. Processes the $_FILES array posted when uploading files, moving valid one to the specified directory. Compressed files are decompressed. Parameters `$files` Array of files to be uploaded. `$dir` Destination path, one of 'src' or 'dest'. Returns string Message with details. See See PHP documentation: POST method uploads. Todo This will be replaced soon!
`public array`	# `imageExtensions( )` Returns a list of file extensions for supported images Returns a list of file extensions for supported images Returns array Array of file extensions.
`public`	# `setImageExtensions( array $extensions )` Sets the list of image extensions. Sets the list of image extensions. Files with these extensions under the user's source folder will be shown under available images. Whenever the image extensions are changed, the files and the selected files will be reset. Only exception is when the list of image extensions is replaced by itself. Parameters `$extensions` Array of file extensions (strings)
`public`	# `setDefaultImageExtensions( )` Sets the image extensions from the list of valid image extensions. Sets the image extensions from the list of valid image extensions.
`public boolean`	# `isImage( string $filename )` Checks whether the filename extension matches the currently selected file format. Checks whether the filename extension matches the currently selected file format. Parameters `$filename` File name to be checked. Returns boolean True if the file extension matches the file format, false otherwise.
`public boolean`	# `isValidImage( string $filename, boolean $alsoExtras = false )` Checks whether the file name is of a valid type. Checks whether the file name is of a valid type. Parameters `$filename` The file name to be checked. `$alsoExtras` If true, consider also extensions as ids or ids.gz. Returns boolean True if the filename is of a valid type, false otherwise.
`public string`	# `getCompressedArchiveType( string $filename )` Returns the archive type of a filename, if it is a valid known compressed archive. Returns the archive type of a filename, if it is a valid known compressed archive. Parameters `$filename` The file name to be checked. Returns string The archive type if the filename is valid archive, "" otherwise.
`public string`	# `getValidArchiveTypesAsString( )` Returns all archive types as string. Returns all archive types as string. Returns string String containing all archive types.
`public array`	# `getSubImages( array $files )` When the selected file type is one that can contain sub-images (like LIF), the already built list of $this->files is extended to show all the available sub-images. This is done by querying HuCore. When the selected file type is one that can contain sub-images (like LIF), the already built list of $this->files is extended to show all the available sub-images. This is done by querying HuCore. Parameters `$files` Array of file names that have to be inspected for sub-images. Returns array Updated array of file names with sub-images.
`public array`	# `getMetaDataFromFiles( array $files )` Some files like ICS can report their metadata without having to open the whole image, which is good e.g. to see the compatibility of the selected PSF with the current Parameter Setting. This is done by querying HuCore. Some files like ICS can report their metadata without having to open the whole image, which is good e.g. to see the compatibility of the selected PSF with the current Parameter Setting. This is done by querying HuCore. Parameters `$files` Array of file paths (relative to the source folder). Returns array N-dimensional array of metadata per file.
`public array`	# `getMetaData( string $type = "ics", string $file = "all" )` Some files like ICS can report their metadata without having to open the whole image, which is good e.g. to see the compatibility of the selected PSF with the current Parameter Setting. This is done by querying HuCore. Some files like ICS can report their metadata without having to open the whole image, which is good e.g. to see the compatibility of the selected PSF with the current Parameter Setting. This is done by querying HuCore. Parameters `$type` File type, default is "ics". `$file` This can be a file name for the file to be inspected, or "all" to inspect all the files of type $type that are in the source folder. Returns array N-dimensional array of metadata per file.
`public string`	# `getImageOptionLine( string $file, integer $index, string $dir, string $type, integer $ref = 0, integer $data = 1 )` Generates a html line for a form listing images in the server Generates a html line for a form listing images in the server Parameters `$file` Image file name. `$index` Unused Index in the file name array. `$dir` Unused Destination directory, one of 'src', or 'dst'. `$type` Unused Type of the image, e.g. 'preview'. `$ref` Unused Default is 0. `$data` Unused Default = 1. Returns string The html code for the form. Todo Check why this function taks 6 parameters and uses only one.
`public string`	# `getImageAction( string $file, integer $index, string $dir, string $type, integer $ref = 0, integer $data = 1 )` Generates a javascript command to show an image preview. Generates a javascript command to show an image preview. Parameters `$file` Image file name. `$index` Index in the file name array. `$dir` Destination directory, one of 'src', or 'dst'. `$type` Type of the image, e.g. 'preview'. `$ref` Default is 0. `$data` Default = 1. Returns string The javascript code.
`public string`	# `imgPreview( string $image, string $dir, string $type = "preview_xy", boolean $escape = true )` Generates a link to retrieve an image thumbnail, which is a jpg file saved near the file itself. Generates a link to retrieve an image thumbnail, which is a jpg file saved near the file itself. Parameters `$image` Image file name. `$dir` Destination directory, one of 'src' or 'dst'. `$type` Type of thumbnail, one of 'preview_xy', 'preview_xz', 'preview_yz'; default is 'preview_xy'. `$escape` If true, the code is escaped to be used in Javascript code. Returns string An link to securely get the thumbnail.
`public string`	# `viewStrip( string $file, string $type = "stack.compare", string $dir = "dest", boolean $frame = false, integer $margin = 25 )` Shows stacks and time series saved as jpeg strips in a css container. Inspired by the paperbird code by Rom�n Cort�s: Shows stacks and time series saved as jpeg strips in a css container. Inspired by the paperbird code by Rom�n Cort�s: Parameters `$file` Image file name. `$type` Type of the strip, one of 'stack.compare', 'tSeries.compare', 'preview_yz'; default is 'stack.compare'. `$dir` Destination directory, one of 'src' or 'dest', default is 'dest'. `$frame` True to draw a frame, false otherwise. `$margin` Thickness of the margin around th strip, default is 25. Returns string HTML code to be output to the page. See http://www.romancortes.com/blog/css-paper-bird/
`public string`	# `previewPage( string $file, string $op = "close", string $mode = "MIP", integer $size = 400 )` Creates the preview page for the file browser. Creates the preview page for the file browser. Parameters `$file` Image file name. `$op` Operation, one of 'close' or 'home'. Default is "close". `$mode` Display mode. One of "MIP", "parameters", "log", "SFP", "stack", "tSeries", "history", "remarks". Default is "MIP". `$size` Size of the thumbnail. Default is 400. Returns string HTML code (whole page).
`public string`	# `compareResult( string $file, integer\|string $size = "400", string $op = "close", string $mode = "MIP" )` Shows original/result previews side by side. Shows original/result previews side by side. Parameters `$file` Image file name. `$size` Size of the thumbnail. Default is 400 `$op` Operation, one of 'close' or 'home'. Default is "close". `$mode` Display mode. One of "MIP, "SFP", "stack", "tSeries", "log", "history", "remarks". Default is "MIP". Returns string HTML code (whole page).
`public string`	# `genPreview( string $file, string $src, string $dest, integer $index, integer\|string $sizes = "preview", string\|integer $data = 0 )` Calls hucore to open an image and generate a jpeg preview. Calls hucore to open an image and generate a jpeg preview. Parameters `$file` Image file name. `$src` Directory, one of 'src' or 'dest'. `$dest` Directory, one of 'src' or 'dest'. `$index` Index. `$sizes` Either an integer, or "preview". Default = "preview". `$data` Either some data (unclear) or 0. Default = 0. Returns string HTML page (complete).
`public string`	# `getThumbnail( string $file, string $dir )` Serves a certain file from the dest directory. Intended to serve jpg thumbails in combination with imgThumbnail. Serves a certain file from the dest directory. Intended to serve jpg thumbails in combination with imgThumbnail. Parameters `$file` Image file name. `$dir` Directory, either 'src' or 'dest'. Returns string Served binary file.
`public string`	# `getMovie( string $file, string $dir = "dest" )` Serves an existing AVI movie. Serves an existing AVI movie. Parameters `$file` Image file name. `$dir` Directory, either 'src' or 'dest'. Default is 'dest'. Returns string Served binary file.
`public boolean`	# `hasSelection( )` Returns true if at least one file is selected. Returns true if at least one file is selected. Returns boolean True if at least one file is selected.
`public boolean`	# `folderContains( string $folder, string $filename )` Checks if a folder contains a given file name. Checks if a folder contains a given file name. Parameters `$folder` Folder name `$filename` File name. Returns boolean True if the folder contains the file name.
`public boolean`	# `folderContainsNewerFile( string $folder, string $date )` Checks if a folder contains newer files than a given date. Checks if a folder contains newer files than a given date. Parameters `$folder` Directory to be checked. `$date` Date string. Returns boolean True if at least one file is more recent than date.
`public array`	# `createHardLinksToSharedPSFs( array $psfFiles, string $targetUser )` Create hard links into the psf_sharing/buffer folder from the folder of the sharing user and return an array of full paths created links. Create hard links into the psf_sharing/buffer folder from the folder of the sharing user and return an array of full paths created links. Parameters `$psfFiles` Array of psf files paths relatives to current user. `$targetUser` name of the target user. Returns array Array of destination PSF paths.
`public array`	# `createHardLinksFromSharedPSFs( array $psfFiles, string $targetUser, string $previousUser )` Create hard links into the folder of the target user from the psf_sharing/buffer folder and return an array of full paths created links. Create hard links into the folder of the target user from the psf_sharing/buffer folder and return an array of full paths created links. Parameters `$psfFiles` array of psf files paths relatives to current user. `$targetUser` Name of the target user. `$previousUser` Name of the previous (source) user. Returns array Array of destination PSF paths.
`public static`	# `deleteSharedFSPFilesFromBuffer( array $psfFiles )` Delete PSF files (hard links) with given relative path from the psf_sharing/buffer folder. Delete PSF files (hard links) with given relative path from the psf_sharing/buffer folder. Parameters `$psfFiles` Array of PSF files paths relative to the file server root.
`public static string\|null`	# `findCompanionFile( string $file )` Given the name of either an ics or and ids file, returns the name of the companion. Given the name of either an ics or and ids file, returns the name of the companion. The companion file must exist. Parameters `$file` File name with either .ics or .ids extension. The case might be different (e.g. .ICS). Returns string\|null Full fine name of the companion file, if it exist; NULL otherwise.
`public array`	# `getPSFiles( )` Return all files with extension ".ics" and ".h5" found by recursive scan of the source folder. Return all files with extension ".ics" and ".h5" found by recursive scan of the source folder. Returns array Array of file names.
`public static boolean\|null`	# `is_dir_empty( string $dir )` Check if a directory is empty. Check if a directory is empty. Parameters `$dir` Full path to directory to check. Returns boolean\|null True if the directory is empty, False if it is not; False if it is not readable or does not exist.

Namespaces

Classes

Functions

Class Fileserver

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