public
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__construct( )
ParameterSetting constructor.
ParameterSetting constructor.
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public static
string
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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
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public static
string
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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.
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public static
string
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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
Overrides
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public static
string
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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
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
array
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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.
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public
array
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imageParameterNames( )
Returns all Image Parameter names.
Returns all Image Parameter names.
Returns
array Array of Image Parameter names.
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public
array
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microscopeParameterNames( )
Returns all Microscope Parameter names.
Returns all Microscope Parameter names.
Returns
array Array of Microscope Parameter names.
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public
array
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stedParameterNames( )
Returns all STED Parameter names.
Returns all STED Parameter names.
Returns
array Array of STED Parameter names.
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public
array
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spimParameterNames( )
Returns all SPIM Parameter names.
Returns all SPIM Parameter names.
Returns
array Array of SPIM Parameter names.
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public
array
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capturingParameterNames( )
Returns all Capture Parameter names.
Returns all Capture Parameter names.
Returns
array Array of Capture Parameter names.
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public
array
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correctionParameterNames( )
Returns all Correction Parameter names.
Returns all Correction Parameter names.
Returns
array Array of Correction Parameter names.
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public
array
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pixelSizeCalculationParameterNames( )
Returns all Pixel Size Calculation Parameter names.
Returns all Pixel Size Calculation Parameter names.
Returns
array Array of Pixel Size Calculation Parameter names.
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public
string
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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.
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public
array|false
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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.
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public
array
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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.
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public
array
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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.
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public
array
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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.
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public
boolean
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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.
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public
array
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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.
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public
array
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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.
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public
array
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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.
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public
boolean
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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.
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public
boolean
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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
Todo
Check if this is still in use.
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public
boolean
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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.
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public
integer
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numberOfChannels( )
Returns the number of channels of the Setting.
Returns the number of channels of the Setting.
Returns
integer The number of channels.
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public
string
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
boolean
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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.
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public
integer
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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!
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public
float
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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.
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public
float
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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.
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public
float
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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.
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public
float
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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.
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public static
array
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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.
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public static
array
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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.
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public
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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'.
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