Class ParameterSetting

A ParameterSetting is a complete set of microscope, image, SPIM, STED, aberration correction, pixel size calculation and capture parameters.

hrm\setting\base\Setting

hrm\setting\ParameterSetting

Direct known subclasses

hrm\setting\JobParameterSetting

Namespace: hrm\setting
Package: hrm
Located at setting/ParameterSetting.php

Methods summary

`public`	# `__construct( )` ParameterSetting constructor. ParameterSetting constructor.
`public static string`	# `table( )` Returns the name of the database table in which the list of Setting names are stored. Returns the name of the database table in which the list of Setting names are stored. Besides the name, the table contains the Setting's name, owner and the standard (default) flag. Returns string The table name. Throws Exception This method must be reimplemented. Overrides `hrm\setting\base\Setting::table`
`public static string`	# `sharedTable( )` Returns the name of the database table in which the list of shared Setting names are stored. Returns the name of the database table in which the list of shared Setting names are stored. Returns string The shared table name.
`public static string`	# `parameterTable( )` Returns the name of the database table in which all the Parameters for the Settings stored in the table specified in table(). Returns the name of the database table in which all the Parameters for the Settings stored in the table specified in table(). Returns string The parameter table name. Throws Exception This method must be reimplemented. See `hrm\setting\ParameterSetting::table()` Overrides `hrm\setting\base\Setting::parameterTable`
`public static string`	# `sharedParameterTable( )` Returns the name of the database table to use for sharing settings. Returns the name of the database table to use for sharing settings. Returns string The shared parameter table name. See `hrm\setting\ParameterSetting::sharedTable()`
`public boolean`	# `checkParameterSetting( )` A general check on the status of the image parameter setting and its compatibility with the selected image format. A general check on the status of the image parameter setting and its compatibility with the selected image format. Returns boolean True if the setting is OK, false otherwise.
`public boolean`	# `checkPostedImageParameters( array $postedParameters )` Checks that the posted Image Parameters are all defined and valid. Checks that the posted Image Parameters are all defined and valid. These Parameters must all be defined. Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public boolean`	# `checkPostedMicroscopyParameters( array $postedParameters )` Checks that the posted Microscopy Parameters are all defined and valid. Checks that the posted Microscopy Parameters are all defined and valid. These Parameter might have different confidence levels Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public boolean`	# `checkPostedSpimParameters( array $postedParameters )` Checks that the posted SPIM Parameters are all defined and valid. Checks that the posted SPIM Parameters are all defined and valid. Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public boolean`	# `checkPostedStedParameters( array $postedParameters )` Checks that the posted STED Parameters are all defined and valid. Checks that the posted STED Parameters are all defined and valid. Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public boolean`	# `checkPostedCapturingParameters( array $postedParameters )` Checks that the posted Capturing Parameters are all defined and valid. Checks that the posted Capturing Parameters are all defined and valid. Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public boolean`	# `checkPostedAberrationCorrectionParameters( array $postedParameters )` Checks that the posted Aberration Correction Parameters are all defined and valid. Checks that the posted Aberration Correction Parameters are all defined and valid. Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public boolean`	# `checkPostedCalculatePixelSizeParameters( array $postedParameters )` Checks that the posted Calculate Pixel Size Parameters are all defined and valid. Checks that the posted Calculate Pixel Size Parameters are all defined and valid. Parameters `$postedParameters` The array of posted parameters. Returns boolean True if all Parameters are defined and valid, false otherwise.
`public array`	# `getAberractionCorrectionParameters( )` Returns the Parameter values needed for the aberration correction. Returns the Parameter values needed for the aberration correction. The Paramters are returned in an array; the keys are the Parameter names. Returns array with all Parameter values for the aberration correction.
`public array`	# `imageParameterNames( )` Returns all Image Parameter names. Returns all Image Parameter names. Returns array Array of Image Parameter names.
`public array`	# `microscopeParameterNames( )` Returns all Microscope Parameter names. Returns all Microscope Parameter names. Returns array Array of Microscope Parameter names.
`public array`	# `stedParameterNames( )` Returns all STED Parameter names. Returns all STED Parameter names. Returns array Array of STED Parameter names.
`public array`	# `spimParameterNames( )` Returns all SPIM Parameter names. Returns all SPIM Parameter names. Returns array Array of SPIM Parameter names.
`public array`	# `capturingParameterNames( )` Returns all Capture Parameter names. Returns all Capture Parameter names. Returns array Array of Capture Parameter names.
`public array`	# `correctionParameterNames( )` Returns all Correction Parameter names. Returns all Correction Parameter names. Returns array Array of Correction Parameter names.
`public array`	# `pixelSizeCalculationParameterNames( )` Returns all Pixel Size Calculation Parameter names. Returns all Pixel Size Calculation Parameter names. Returns array Array of Pixel Size Calculation Parameter names.
`public string`	# `displayString( integer $numberOfChannels = 0, string\|null $micrType = NULL )` Displays the setting as a text containing Parameter names and their values. Displays the setting as a text containing Parameter names and their values. Parameters `$numberOfChannels` Number of channels (ignored). `$micrType` Microscope type (ignored). Returns string Parameter names and their values as a string.
`public array\|false`	# `calculateNyquistRate( )` Asks HuCore to calculate the ideal (Nyquist) sampling rate for the current conditions. Asks HuCore to calculate the ideal (Nyquist) sampling rate for the current conditions. Returns array\|false An array with the ideal XY and Z sampling, or false if the sampling could not be calculated due to missing values.
`public array`	# `threeDimensionalGeometries( )` Returns all 3-D geometries (i.e. 'XYZ', 'XYZ - time') Returns all 3-D geometries (i.e. 'XYZ', 'XYZ - time') Returns array The 3D geometries. Todo Check if this is still in use.
`public array`	# `timeSeriesGeometries( )` Returns all time series geometries (i.e. 'XY - time', 'XYZ - time') Returns all time series geometries (i.e. 'XY - time', 'XYZ - time') Returns array The time series geometries. Todo Check if this is still in use.
`public array`	# `fixedGeometryFileFormats( )` Returns all fixed geometry file formats (i.e. those that are 2D) Returns all fixed geometry file formats (i.e. those that are 2D) Returns array The fixed geometry file formats. Todo Check if this is still in use.
`public boolean`	# `isFixedGeometryFormat( )` Checks whether currently chosen file format has fixed geometry. Checks whether currently chosen file format has fixed geometry. Returns boolean True if the chosen file format has fixed geometry, false otherwise.
`public array`	# `singleChannelFileFormats( )` Returns the file formats that support single channel images. Returns the file formats that support single channel images. Returns array Array of file formats. Todo Check if this is still in use.
`public array`	# `multiChannelFileFormats( )` Returns the file formats that support multi-channel images. Returns the file formats that support multi-channel images. Returns array Array of of multi-channel file formats. Todo Check if this is still in use.
`public array`	# `variableChannelFileFormats( )` Returns the file formats that support a variable number of channels per file. Returns the file formats that support a variable number of channels per file. Returns array Array of file formats that support variable number of channels. Todo Check if this is still in use.
`public boolean`	# `isMultiChannel( )` Checks whether current Setting is for multi-channel file formats Checks whether current Setting is for multi-channel file formats Returns boolean True if the number of channels set for current Setting is > 1, false otherwise. Todo Check if this is still in use.
`public boolean`	# `isVariableChannelFormat( )` Checks whether currently selected file format is variable channel Checks whether currently selected file format is variable channel Returns boolean True if the currently selected file format is variable channel, false otherwise. See `hrm\setting\ParameterSetting::variableChannelFileFormats()` Todo Check if this is still in use.
`public boolean`	# `isTif( )` Checks whether currently selected file format is one of the TIFF variants. Checks whether currently selected file format is one of the TIFF variants. Returns boolean True if the currently selected file format is a TIFF variant. false othewise. Todo Check if this is still in use.
`public integer`	# `numberOfChannels( )` Returns the number of channels of the Setting. Returns the number of channels of the Setting. Returns integer The number of channels.
`public string`	# `microscopeType( )` Returns the main microscope mode.. Returns the main microscope mode.. Returns string One of confocal, widefield, STED, STED 3D, spinning disk, SPIM or multiphoton.
`public boolean`	# `isNipkowDisk( )` Checks whether the currently selected microscope type is spinning (Nipkow) disk confocal. Checks whether the currently selected microscope type is spinning (Nipkow) disk confocal. Returns boolean true if the currently selected microscope type is spinning (Nipkow) disk, false otherwise.
`public boolean`	# `isTwoPhoton( )` Checks whether the currently selected microscope type is 2-Photon Checks whether the currently selected microscope type is 2-Photon Returns boolean True if the currently selected microscope type is 2-Photon, false otherwise.
`public boolean`	# `isSinglePointConfocal( )` Checks whether the currently selected microscope type is single-point confocal. Checks whether the currently selected microscope type is single-point confocal. Returns boolean True if the currently selected microscope type is single-point confocal, false otherwise.
`public boolean`	# `isSted( )` Checks whether the currently selected microscope type is sted. Checks whether the currently selected microscope type is sted. Returns boolean True if the currently selected microscope type is sted, false otherwise.
`public boolean`	# `isSted3D( )` Checks whether the currently selected microscope type is sted 3D. Checks whether the currently selected microscope type is sted 3D. Returns boolean True if the currently selected microscope type is sted 3D, false otherwise.
`public boolean`	# `isSpim( )` Checks whether the currently selected microscope type is spim. Checks whether the currently selected microscope type is spim. Returns boolean True if the currently selected microscope type is spim, false otherwise.
`public boolean`	# `isMultiPointConfocal( )` Checks whether the currently selected microscope type is spinning (Nipkow) disk confocal. Checks whether the currently selected microscope type is spinning (Nipkow) disk confocal. Returns boolean True if the currently selected microscope type is spinning (Nipkow) disk, false otherwise.
`public boolean`	# `isWidefield( )` Checks whether the currently selected microscope type is widefield. Checks whether the currently selected microscope type is widefield. Returns boolean True if the currently selected microscope type is widefield, false otherwise.
`public boolean`	# `isWidefieldOrMultiPoint( )` Checks whether the currently selected microscope type is either widefield of spinning disk. Checks whether the currently selected microscope type is either widefield of spinning disk. Returns boolean True if the currently selected microscope type is either widefield of spinning disk, false otherwise.
`public boolean`	# `isTwoPhotonOrSinglePoint( )` Checks whether the currently selected microscope type is either 2-Photon or single-point confocal. Checks whether the currently selected microscope type is either 2-Photon or single-point confocal. Returns boolean True if the currently selected microscope type is either 2-Photon or single-point confocal, false otherwise.
`public boolean`	# `isMultiPointOrSinglePointConfocal( )` Checks whether the currently selected microscope type is any type of confocal. Checks whether the currently selected microscope type is any type of confocal. Returns boolean True if the currently selected microscope type is any type of confocal, false otherwise.
`public boolean`	# `hasPinhole( )` This determines which microscope types have a pinhole This determines which microscope types have a pinhole Returns boolean True if the microscope contains a pinhole, false otherwise.
`public integer`	# `pixelSize( )` Returns the pixel size (the value of CCDCaptorSizeX) in nm. Returns the pixel size (the value of CCDCaptorSizeX) in nm. Returns integer Pixel size in nm, Todo This is redundant!
`public float`	# `sampleSizeX( )` Returns the sample size in X direction in um. Returns the sample size in X direction in um. This is simply pixelSize() / 1000. Returns float Sample size in um.
`public float`	# `sampleSizeY( )` Returns the sample size in Y direction in um. Returns the sample size in Y direction in um. This just returns the value in X direction. Returns float Sample size in um.
`public float`	# `sampleSizeZ( )` Returns the sample size in um in Z direction. Returns the sample size in um in Z direction. This is the value of the z-step size / 1000. Returns float Sample size in um.
`public float`	# `sampleSizeT( )` Returns the time interval between consecutive time points in a time series in seconds. Returns the time interval between consecutive time points in a time series in seconds. Returns float Time interval in seconds.
`public static array`	# `getTemplatesSharedWith( string $username )` Get the list of templates shared with the given user. Get the list of templates shared with the given user. Parameters `$username` Name of the user to query for. Returns array List of shared templates with the user.
`public static array`	# `getTemplatesSharedBy( string $username )` Get the list of templates shared by the given user. Get the list of templates shared by the given user. Parameters `$username` Name of the user to query for. Returns array List of shared templates by the user.
`public`	# `parseParamsFromHuCore( array $huArray )` Map Huygens parameters to HRM parameters. Map Huygens parameters to HRM parameters. Parameters `$huArray` An array with the result of 'image setp -tclReturn'.

Methods inherited from hrm\setting\base\Setting

__clone(), beDefault(), copyParameterFrom(), isDefault(), load(), message(), name(), owner(), parameter(), parameterNames(), resetDefault(), save(), set(), setName(), setNumberOfChannels(), setOwner(), shareWith()

Namespaces

Classes

Class ParameterSetting

Direct known subclasses

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