Package omero.api

Interface _RawPixelsStoreOperationsNC

  • All Superinterfaces:
    _PyramidServiceOperationsNC, _ServiceInterfaceOperationsNC, _StatefulServiceInterfaceOperationsNC
    All Known Subinterfaces:
    RawPixelsStore
    All Known Implementing Classes:
    _RawPixelsStoreDisp, _RawPixelsStoreTie, BfPixelsStoreI
    public interface _RawPixelsStoreOperationsNC
extends _PyramidServiceOperationsNC
    Binary data provider. Initialized with the ID of a Pixels instance, this service can provide various slices, stacks, regions of the 5-dimensional (X-Y planes with multiple Z-sections and Channels over Time). The byte array returned by the getter methods and passed to the setter methods can and will be interpreted according to results of getByteWidth, isFloat, and isSigned.

    Read-only caveat: Mutating methods (set*) are only available during the first access. Once the Pixels data has been successfully saved (via the save or close methods on this interface), then the data should be treated read-only. If Pixels data writing fails and the service is inadvertently closed, delete the Pixels object, and create a new one. Any partially written data will be removed.

    • Method Detail

      • setPixelsId_async

        void setPixelsId_async​(AMD_RawPixelsStore_setPixelsId __cb,
                       long pixelsId,
                       boolean bypassOriginalFile)
                throws ServerError
        Initializes the stateful service for a given Pixels set.
        Parameters:
        __cb - The callback object for the operation.
        pixelsId - Pixels set identifier.
        Throws:
        ServerError

      • prepare_async

        void prepare_async​(AMD_RawPixelsStore_prepare __cb,
                   java.util.List<java.lang.Long> pixelsIds)
            throws ServerError
        Prepares the stateful service with a cache of loaded Pixels objects. This method is designed to combat query overhead, where many sets of Pixels are to be read from or written to, by loading all the Pixels sets at once. Multiple calls will result in the existing cache being overwritten.
        Parameters:
        __cb - The callback object for the operation.
        pixelsIds - Pixels IDs to cache.
        Throws:
        ServerError

      • getRowSize_async

        void getRowSize_async​(AMD_RawPixelsStore_getRowSize __cb)
               throws ServerError
        Retrieves the in memory size of a row or scanline of pixels in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        Throws:
        ServerError

      • getStackSize_async

        void getStackSize_async​(AMD_RawPixelsStore_getStackSize __cb)
                 throws ServerError
        Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        Throws:
        ServerError

      • getTimepointSize_async

        void getTimepointSize_async​(AMD_RawPixelsStore_getTimepointSize __cb)
                     throws ServerError
        Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        Throws:
        ServerError

      • getRowOffset_async

        void getRowOffset_async​(AMD_RawPixelsStore_getRowOffset __cb,
                        int y,
                        int z,
                        int c,
                        int t)
                 throws ServerError
        Retrieves the offset for a particular row or scanline in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        y - offset across the Y-axis of the pixel buffer.
        c - offset across the C-axis of the pixel buffer.
        Throws:
        ServerError

      • getPlaneOffset_async

        void getPlaneOffset_async​(AMD_RawPixelsStore_getPlaneOffset __cb,
                          int z,
                          int c,
                          int t)
                   throws ServerError
        Retrieves the offset for a particular 2D image plane in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        z - offset across the Z-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        ServerError

      • getStackOffset_async

        void getStackOffset_async​(AMD_RawPixelsStore_getStackOffset __cb,
                          int c,
                          int t)
                   throws ServerError
        Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        c - offset across the C-axis of the pixel buffer.
        Throws:
        ServerError

      • getTimepointOffset_async

        void getTimepointOffset_async​(AMD_RawPixelsStore_getTimepointOffset __cb,
                              int t)
                       throws ServerError
        Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        t - offset across the T-axis of the pixel buffer.
        Throws:
        ServerError

      • getTile_async

        void getTile_async​(AMD_RawPixelsStore_getTile __cb,
                   int z,
                   int c,
                   int t,
                   int x,
                   int y,
                   int w,
                   int h)
            throws ServerError
        Retrieves a tile from this pixel buffer.
        Parameters:
        __cb - The callback object for the operation.
        z - offset across the Z-axis of the pixel buffer.
        t - offset across the T-axis of the pixel buffer.
        y - Top left corner of the tile, Y offset.
        h - Height of the tile.
        Throws:
        ServerError

      • getHypercube_async

        void getHypercube_async​(AMD_RawPixelsStore_getHypercube __cb,
                        java.util.List<java.lang.Integer> offset,
                        java.util.List<java.lang.Integer> size,
                        java.util.List<java.lang.Integer> step)
                 throws ServerError
        Retrieves a n-dimensional block from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        offset - offset for each dimension within pixel store.
        step - needed of each dimension (dependent on dimension).
        Throws:
        ServerError

      • getRegion_async

        void getRegion_async​(AMD_RawPixelsStore_getRegion __cb,
                     int size,
                     long offset)
              throws ServerError
        Retrieves a region from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        size - byte width of the region to retrieve.
        Throws:
        ServerError

      • getRow_async

        void getRow_async​(AMD_RawPixelsStore_getRow __cb,
                  int y,
                  int z,
                  int c,
                  int t)
           throws ServerError
        Retrieves a particular row or scanline from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        y - offset across the Y-axis of the pixel store.
        c - offset across the C-axis of the pixel store.
        Throws:
        ServerError

      • getCol_async

        void getCol_async​(AMD_RawPixelsStore_getCol __cb,
                  int x,
                  int z,
                  int c,
                  int t)
           throws ServerError
        Retrieves a particular column from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        x - offset across the X-axis of the pixel store.
        c - offset across the C-axis of the pixel store.
        Throws:
        ServerError

      • getPlane_async

        void getPlane_async​(AMD_RawPixelsStore_getPlane __cb,
                    int z,
                    int c,
                    int t)
             throws ServerError
        Retrieves a particular 2D image plane from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        z - offset across the Z-axis of the pixel store.
        t - offset across the T-axis of the pixel store.
        Throws:
        ServerError

      • getPlaneRegion_async

        void getPlaneRegion_async​(AMD_RawPixelsStore_getPlaneRegion __cb,
                          int z,
                          int c,
                          int t,
                          int size,
                          int offset)
                   throws ServerError
        Retrieves a region from a given plane from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        z - offset across the Z-axis of the pixel store.
        t - offset across the T-axis of the pixel store.
        offset - the offset at which to retrieve size pixels.
        Throws:
        ServerError

      • getStack_async

        void getStack_async​(AMD_RawPixelsStore_getStack __cb,
                    int c,
                    int t)
             throws ServerError
        Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        c - offset across the C-axis of the pixel store.
        Throws:
        ServerError

      • getTimepoint_async

        void getTimepoint_async​(AMD_RawPixelsStore_getTimepoint __cb,
                        int t)
                 throws ServerError
        Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        t - offset across the T-axis of the pixel store.
        Throws:
        ServerError

      • setTile_async

        void setTile_async​(AMD_RawPixelsStore_setTile __cb,
                   byte[] buf,
                   int z,
                   int c,
                   int t,
                   int x,
                   int y,
                   int w,
                   int h)
            throws ServerError
        Sets a tile in this pixel buffer.
        Parameters:
        __cb - The callback object for the operation.
        buf - A byte array of the data.
        c - offset across the C-axis of the pixel buffer.
        x - Top left corner of the tile, X offset.
        w - Width of the tile.
        Throws:
        IOException - if there is a problem writing to the pixel buffer.
        BufferOverflowException - if an attempt is made to write off the end of the file. See Read-only caveat under RawPixelsStore
        ServerError

      • setRegion_async

        void setRegion_async​(AMD_RawPixelsStore_setRegion __cb,
                     int size,
                     long offset,
                     byte[] buf)
              throws ServerError
        Sets a region in this pixel buffer.
        Parameters:
        __cb - The callback object for the operation.
        size - byte width of the region to set.
        buf - a byte array of the data. See Read-only caveat under RawPixelsStore
        Throws:
        ServerError

      • setRow_async

        void setRow_async​(AMD_RawPixelsStore_setRow __cb,
                  byte[] buf,
                  int y,
                  int z,
                  int c,
                  int t)
           throws ServerError
        Sets a particular row or scanline in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        buf - a byte array of the data comprising this row or scanline.
        z - offset across the Z-axis of the pixel store.
        t - offset across the T-axis of the pixel store. See Read-only caveat under RawPixelsStore
        Throws:
        ServerError

      • setPlane_async

        void setPlane_async​(AMD_RawPixelsStore_setPlane __cb,
                    byte[] buf,
                    int z,
                    int c,
                    int t)
             throws ServerError
        Sets a particular 2D image plane in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        buf - a byte array of the data comprising this 2D image plane.
        c - offset across the C-axis of the pixel store.
        Throws:
        ServerError

      • setStack_async

        void setStack_async​(AMD_RawPixelsStore_setStack __cb,
                    byte[] buf,
                    int z,
                    int c,
                    int t)
             throws ServerError
        Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        buf - a byte array of the data comprising this stack.
        t - offset across the T-axis of the pixel store. See Read-only caveat under RawPixelsStore
        Throws:
        ServerError

      • setTimepoint_async

        void setTimepoint_async​(AMD_RawPixelsStore_setTimepoint __cb,
                        byte[] buf,
                        int t)
                 throws ServerError
        Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        buf - a byte array of the data comprising this timepoint.
        Throws:
        ServerError

      • getHistogram_async

        void getHistogram_async​(AMD_RawPixelsStore_getHistogram __cb,
                        int[] channels,
                        int binCount,
                        boolean globalRange,
                        PlaneDef plane)
                 throws ServerError
        Retrieves the histogram data for the specified plane and channels. This method can currently only handle non-pyramid images.
        Parameters:
        __cb - The callback object for the operation.
        channels - the channels to generate the histogram data for
        plane - the plane (optional, default: whole region of first z/t plane)
        Throws:
        ServerError

      • findMinMax_async

        void findMinMax_async​(AMD_RawPixelsStore_findMinMax __cb,
                      int[] channels)
               throws ServerError
        Find the minimum and maximum pixel values for the specified channels by iterating over a full plane. In case of multi-z/t images only the 'middle' plane with index maxZ/2, respectively maxT/2 is taken into account. Note: This method can currently only handle non-pyramid images, otherwise an empty map will be returned.
        Parameters:
        __cb - The callback object for the operation.
        channels - the channels
        Throws:
        ServerError

      • save_async

        void save_async​(AMD_RawPixelsStore_save __cb)
         throws ServerError
        Save the current state of the pixels, updating the SHA1. This should only be called AFTER all data is successfully set. Future invocations of set methods may be disallowed. This read-only status will allow background processing (generation of thumbnails, compression, etc.) to begin. More information under RawPixelsStore. A null instance will be returned if no save was performed.
        Parameters:
        __cb - The callback object for the operation.
        Throws:
        ServerError