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help_SBReadFile.txt
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Help on module SBReadFile:
NAME
SBReadFile
CLASSES
builtins.object
SBReadFile
enum.Enum(builtins.object)
EROI_Shapes
class EROI_Shapes(enum.Enum)
| EROI_Shapes(value, names=None, *, module=None, qualname=None, type=None, start=1)
|
| Enum with shapes retuirned from GetROIAnnotation
|
| Method resolution order:
| EROI_Shapes
| enum.Enum
| builtins.object
|
| Data and other attributes defined here:
|
| eArrow = <EROI_Shapes.eArrow: 6>
|
| eEllipse = <EROI_Shapes.eEllipse: 5>
|
| eError = <EROI_Shapes.eError: 7>
|
| eLine = <EROI_Shapes.eLine: 2>
|
| ePoint = <EROI_Shapes.ePoint: 1>
|
| ePolygon = <EROI_Shapes.ePolygon: 4>
|
| eRectangle = <EROI_Shapes.eRectangle: 3>
|
| ----------------------------------------------------------------------
| Data descriptors inherited from enum.Enum:
|
| name
| The name of the Enum member.
|
| value
| The value of the Enum member.
|
| ----------------------------------------------------------------------
| Readonly properties inherited from enum.EnumMeta:
|
| __members__
| Returns a mapping of member name->value.
|
| This mapping lists all enum members, including aliases. Note that this
| is a read-only view of the internal mapping.
class SBReadFile(builtins.object)
| A Class to Read Slide Book Format 7 Files
|
| Methods defined here:
|
| GetAuxDataNumElements(self, inCaptureIndex, inChannelIndex)
| Gets the Auxiliary Data number of elements for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| int
| The number of elements
|
| GetAuxDataXMLDescriptor(self, inCaptureIndex, inChannelIndex)
| Gets the Auxiliary Data XML Descriptor for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| str
| The XML Descriptor
|
| GetAuxDoubleData(self, inCaptureIndex, inChannelIndex)
| Gets the Auxiliary Double Data for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| list : float
| The Double Data as a list
|
| GetAuxFloatData(self, inCaptureIndex, inChannelIndex)
| Gets the Auxiliary Float Data for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| list : float
| The Float Data as a list
|
| GetAuxSInt32Data(self, inCaptureIndex, inChannelIndex)
| Gets the Auxiliary Signed Int32 Data for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| list: int
| The Signed Int32 Data as a list
|
| GetAuxSInt64Data(self, inCaptureIndex, inChannelIndex)
| Gets the Auxiliary Signed Int64 Data for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| list: int
| The Signed Int64 Data as a list
|
| GetAuxSerializedData(self, inCaptureIndex, inChannelIndex, inElementIndex)
| Gets the Auxiliary XML Data for an image group and a channel
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inChannelIndex: int
| The channel number
|
| Returns
| -------
| list: str
| The XML Data as a list
|
| GetCaptureDate(self, inCaptureIndex)
| Gets the date of acquisition of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The year
| int
| The month
| int
| The day
| int
| The hour
| int
| The minute
| int
| The second
|
| GetChannelName(self, inCaptureIndex, inChannelIndex)
| Gets the name of a given channel of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| inChannelIndex: int
| The index of the channel. Must be in range(0,number of channels)
|
| Returns
| -------
| str
| The name of the channel
|
| GetElapsedTime(self, inCaptureIndex, inTimepointIndex)
| Gets the elapsed time in ms at a given time point in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inTimepointIndex: int
| The time point number
|
| Returns
| -------
| int
| The elapsed time in ms
|
| GetExposureTime(self, inCaptureIndex, inChannelIndex)
| Gets the exposure time in ms for a particular channel of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| inChannelIndex: int
| The index of the channel. Must be in range(0,number of channels)
|
| Returns
| -------
| int
| The exposure time in ms
|
| GetFRAPAnnotation(self, inCaptureIndex, inTimepointIndex)
| Gets a FRAP Annotation in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| inTimepointIndex: int
| The time point number
|
| Returns
| -------
| int
| the FRAP Shape in the Enum EROI_Shapes
| int
| the number of (x,y) points in the annotation
| list
| list of points
|
| GetFRAPRegion(self, inCaptureIndex, inTimepointIndex, inRegionIndex)
| Gets a FRAP Region in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| inRegionIndex: int
| The index of the desired annotation. Must be in range(0,number of ROI annotations)
|
| inTimepointIndex: int
| The time point number
|
| Returns
| -------
| int
| the FRAP Shape in the Enum EROI_Shapes
| int
| the number of (x,y) points in the annotation
| list
| list of points
|
| GetImageComments(self, inCaptureIndex)
| Gets the comments of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| str
| The comments of the image group
|
| GetImageName(self, inCaptureIndex)
| Gets the name of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| str
| The name of the image group
|
| GetLensName(self, inCaptureIndex)
| Gets the name of the lens of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| str
| The name of the lens
|
| GetMagnification(self, inCaptureIndex)
| Gets the magnification of the lens of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| float
| The magnification of the lens
|
| GetMontageColumn(self, inCaptureIndex, inPositionIndex)
| Gets the number of columns of the montage at a given position in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inPositionIndex: int
| The position of an image whose column is to be retrieved
|
| Returns
| -------
| int
| The column number (first column is 0)
|
| GetMontageRow(self, inCaptureIndex, inPositionIndex)
| Gets the rows of the montage at a given position in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inPositionIndex: int
| The position of an image whose row is to be retrieved
|
| Returns
| -------
| int
| The row number (first row is 0)
|
| GetNumCaptures(self)
| Gets the number of captures (image groups) in the file
|
| Returns
| -------
| int
| The number of captures
|
| GetNumChannels(self, inCaptureIndex)
| Gets the number of channels in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of channels
|
| GetNumFRAPRegions(self, inCaptureIndex, inTimepointIndex)
| Gets the number of FRAP Regions in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| inTimepointIndex: int
| The time point number
|
| Returns
| -------
| int
| The number of ROI Annotations
|
| GetNumPositions(self, inCaptureIndex)
| Gets the number of (montage) positions in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of positions
|
| GetNumROIAnnotations(self, inCaptureIndex)
| Gets the number of ROI Annotations in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of ROI Annotations
|
| GetNumTimepoints(self, inCaptureIndex)
| Gets the number of time points in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of time points
|
| GetNumXColumns(self, inCaptureIndex)
| Gets the number of columns (width) of an image in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of columns or width of the image
|
| GetNumYRows(self, inCaptureIndex)
| Gets the number of rows (height) of an image in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of rows or height of the image
|
| GetNumZPlanes(self, inCaptureIndex)
| Gets the number of z planes of an image in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| int
| The number of z planes of the image
|
| GetROIAnnotation(self, inCaptureIndex, inAnnotationIndex)
| Gets a ROI Annotation in an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| inAnnotationIndex: int
| The index of the desired annotation. Must be in range(0,number of ROI annotations)
|
| Returns
| -------
| int
| the ROI Shape in the Enum EROI_Shapes
| int
| the number of (x,y) points in the annotation
| list
| list of points
|
| GetThumbnail(self, inCaptureIndex)
| Gets the thumbnail
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| numpy uint32 array
| The thumbnail is returned as list of 1024 integers values. Each value is a 32 bit color value. The thumbnail is 32x32 pixels ordered by rows.
|
| GetVoxelSize(self, inCaptureIndex)
| Gets the voxel size in microns of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| Returns
| -------
| float
| The X voxel size in um
| float
| The Y voxel size in um
| float
| The Z voxel size in um
|
| GetXPosition(self, inCaptureIndex, inPositionIndex)
| Gets the X position in microns of the center of an image of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inPositionIndex: int
| The index of the image in the montage, or 0 if all images are at the same location
|
| Returns
| -------
| float
| The X position in um
|
| GetYPosition(self, inCaptureIndex, inPositionIndex)
| Gets the Y position in microns of the center of an image of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inPositionIndex: int
| The index of the image in the montage, or 0 if all images are at the same location
|
| Returns
| -------
| float
| The Y position in um
|
| GetZPosition(self, inCaptureIndex, inPositionIndex, inZPlaneIndex)
| Gets the Z position in microns of the center of an image of an image group
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inPositionIndex: int
| The index of the image in the montage, or 0 if all images are at the same location
|
| Returns
| -------
| float
| The Z position in um
|
| Open(self, inPath, All=True)
| Open a SlideBook file and loads the Metadata
|
| Parameters
| ----------
| inPath : str
| The path of the SlideBook file to open
| Returns
| -------
| bool
| true if file opeend succesfully, else false
|
| ReadImagePlaneBuf(self, inCaptureIndex, inPositionIndex, inTimepointIndex, inZPlaneIndex, inChannelIndex, inAs2D=False)
| Reads a z plane of an image into a numpy array
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
| inPositionIndex: int
| The position of the image. If the image group is not a montage, use 0
| inTimepointIndex: int
| The time point
| inZPlaneIndex: int
| The z plane number
| inChannelIndex: int
| The channel number
| inAs2D: bool, optional
| if True, returna 2D array, otheiws (default) returna 1D array
|
| Returns
| -------
| numpy uint16 array
| The image is returned as 1D numpy uint16 array if inAs2D is false
| Otherwise is returned as a 2D array of (NumRows,NumColumns)
|
| Refresh(self, inCaptureIndex)
| Refresh metadata
|
| Parameters
| ----------
| inCaptureIndex: int
| The index of the image group. Must be in range(0,number of captures)
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| __dict__
| dictionary for instance variables (if defined)
|
| __weakref__
| list of weak references to the object (if defined)
DATA
__copyright__ = 'Copyright (c) 2022, Intelligent Imaging Innovations, ...
__license__ = 'This source code is licensed under the BSD-style...E fi...
FILE
c:\users\nicola papp\perforce\nicola_msi_552\dev\sb_7.0_bcg\sbreadfile\dist\python\format 7\sbreadfile.py