Package ome.services.blitz.repo

Class BfPixelsStoreI

    • Constructor Detail

      • BfPixelsStoreI

        public BfPixelsStoreI​(java.lang.String path,
                      loci.formats.ImageReader bfReader)
               throws java.io.IOException,
                      loci.formats.FormatException
        Deprecated.
        Throws:
        java.io.IOException
        loci.formats.FormatException

    • Method Detail

      • getHypercube_async

        public 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,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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).
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getCol_async

        public void getCol_async​(AMD_RawPixelsStore_getCol __cb,
                         int x,
                         int z,
                         int c,
                         int t,
                         Ice.Current __current)
                  throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getPlaneOffset_async

        public void getPlaneOffset_async​(AMD_RawPixelsStore_getPlaneOffset __cb,
                                 int z,
                                 int c,
                                 int t,
                                 Ice.Current __current)
                          throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getPlaneRegion_async

        public void getPlaneRegion_async​(AMD_RawPixelsStore_getPlaneRegion __cb,
                                 int z,
                                 int c,
                                 int t,
                                 int size,
                                 int offset,
                                 Ice.Current __current)
                          throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getPlaneSize_async

        public void getPlaneSize_async​(AMD_RawPixelsStore_getPlaneSize __cb,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Retrieves the in memory size of a 2D image plane in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getPlane_async

        public void getPlane_async​(AMD_RawPixelsStore_getPlane __cb,
                           int z,
                           int c,
                           int t,
                           Ice.Current __current)
                    throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getRegion_async

        public void getRegion_async​(AMD_RawPixelsStore_getRegion __cb,
                            int size,
                            long offset,
                            Ice.Current __current)
                     throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Retrieves a region from this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        size - byte width of the region to retrieve.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getRowOffset_async

        public void getRowOffset_async​(AMD_RawPixelsStore_getRowOffset __cb,
                               int y,
                               int z,
                               int c,
                               int t,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getRowSize_async

        public void getRowSize_async​(AMD_RawPixelsStore_getRowSize __cb,
                             Ice.Current __current)
                      throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Retrieves the in memory size of a row or scanline of pixels in this pixel store.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getRow_async

        public void getRow_async​(AMD_RawPixelsStore_getRow __cb,
                         int y,
                         int z,
                         int c,
                         int t,
                         Ice.Current __current)
                  throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getStackOffset_async

        public void getStackOffset_async​(AMD_RawPixelsStore_getStackOffset __cb,
                                 int c,
                                 int t,
                                 Ice.Current __current)
                          throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getStackSize_async

        public void getStackSize_async​(AMD_RawPixelsStore_getStackSize __cb,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getStack_async

        public void getStack_async​(AMD_RawPixelsStore_getStack __cb,
                           int c,
                           int t,
                           Ice.Current __current)
                    throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getTimepointOffset_async

        public void getTimepointOffset_async​(AMD_RawPixelsStore_getTimepointOffset __cb,
                                     int t,
                                     Ice.Current __current)
                              throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getTimepointSize_async

        public void getTimepointSize_async​(AMD_RawPixelsStore_getTimepointSize __cb,
                                   Ice.Current __current)
                            throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getTimepoint_async

        public void getTimepoint_async​(AMD_RawPixelsStore_getTimepoint __cb,
                               int t,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getTotalSize_async

        public void getTotalSize_async​(AMD_RawPixelsStore_getTotalSize __cb,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Retrieves the in memory size of the entire pixel store.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • isFloat_async

        public void isFloat_async​(AMD_RawPixelsStore_isFloat __cb,
                          Ice.Current __current)
                   throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Returns whether or not the pixel buffer has floating point pixels.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • isSigned_async

        public void isSigned_async​(AMD_RawPixelsStore_isSigned __cb,
                           Ice.Current __current)
                    throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Returns whether or not the pixel store has signed pixels.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • prepare_async

        public void prepare_async​(AMD_RawPixelsStore_prepare __cb,
                          java.util.List<java.lang.Long> pixelsIds,
                          Ice.Current __current)
                   throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • save_async

        public void save_async​(AMD_RawPixelsStore_save __cb,
                       Ice.Current __current)
                throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setPixelsId_async

        public void setPixelsId_async​(AMD_RawPixelsStore_setPixelsId __cb,
                              long pixelsId,
                              boolean bypassOriginalFile,
                              Ice.Current __current)
                       throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Initializes the stateful service for a given Pixels set.
        Parameters:
        __cb - The callback object for the operation.
        pixelsId - Pixels set identifier.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setPlane_async

        public void setPlane_async​(AMD_RawPixelsStore_setPlane __cb,
                           byte[] buf,
                           int z,
                           int c,
                           int t,
                           Ice.Current __current)
                    throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setRegion_async

        public void setRegion_async​(AMD_RawPixelsStore_setRegion __cb,
                            int size,
                            long offset,
                            byte[] buffer,
                            Ice.Current __current)
                     throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        Sets a region in this pixel buffer.
        Parameters:
        __cb - The callback object for the operation.
        size - byte width of the region to set.
        buffer - a byte array of the data. See Read-only caveat under RawPixelsStore
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setRow_async

        public void setRow_async​(AMD_RawPixelsStore_setRow __cb,
                         byte[] buf,
                         int y,
                         int z,
                         int c,
                         int t,
                         Ice.Current __current)
                  throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setStack_async

        public void setStack_async​(AMD_RawPixelsStore_setStack __cb,
                           byte[] buf,
                           int z,
                           int c,
                           int t,
                           Ice.Current __current)
                    throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setTimepoint_async

        public void setTimepoint_async​(AMD_RawPixelsStore_setTimepoint __cb,
                               byte[] buf,
                               int t,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getHistogram_async

        public void getHistogram_async​(AMD_RawPixelsStore_getHistogram __cb,
                               int[] channels,
                               int binCount,
                               boolean globalRange,
                               PlaneDef plane,
                               Ice.Current __current)
                        throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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)
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • findMinMax_async

        public void findMinMax_async​(AMD_RawPixelsStore_findMinMax __cb,
                             int[] channels,
                             Ice.Current __current)
                      throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • activate_async

        public void activate_async​(AMD_StatefulServiceInterface_activate __cb,
                           Ice.Current __current)
                    throws ServerError
        Deprecated.
        Description copied from interface: _StatefulServiceInterfaceOperations
        Load a service implementation from disk if it was previously passivated. It is unnecessary to call this method since activation happens automatically, but calling this may prevent a short lapse when the service is first accessed after passivation. It is safe to call this method at any time, even when the service is not passivated.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • close_async

        public void close_async​(AMD_StatefulServiceInterface_close __cb,
                        Ice.Current __current)
                 throws ServerError
        Deprecated.
        Description copied from interface: _StatefulServiceInterfaceOperations
        Frees all resources -- passivated or active -- for the given stateful service and removes its name from the object adapter. Any further method calls will fail with a Ice::NoSuchObjectException. Note: with JavaEE, the close method was called publicly, and internally this called destroy(). As of the OmeroBlitz migration, this functionality has been combined.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • passivate_async

        public void passivate_async​(AMD_StatefulServiceInterface_passivate __cb,
                            Ice.Current __current)
                     throws ServerError
        Deprecated.
        Description copied from interface: _StatefulServiceInterfaceOperations
        Causes the blitz server to store the service implementation to disk to free memory. This is typically done automatically by the server when a pre-defined memory limit is reached, but can be used by the client if it clear that a stateful service will not be used for some time. Activation will happen automatically whether passivation was done manually or automatically.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getResolutionLevels_async

        public void getResolutionLevels_async​(AMD_PyramidService_getResolutionLevels __cb,
                                      Ice.Current __current)
                               throws ServerError
        Deprecated.
        Description copied from interface: _PyramidServiceOperations
        Retrieves the number of resolution levels that the backing pixels pyramid contains.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getResolutionDescriptions_async

        public void getResolutionDescriptions_async​(AMD_PyramidService_getResolutionDescriptions __cb,
                                            Ice.Current __current)
                                     throws ServerError
        Deprecated.
        Description copied from interface: _PyramidServiceOperations
        Retrieves a more complete definition of the resolution level in question. The size of this array will be of length getResolutionLevels.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • requiresPixelsPyramid_async

        public void requiresPixelsPyramid_async​(AMD_PyramidService_requiresPixelsPyramid __cb,
                                        Ice.Current __current)
                                 throws ServerError
        Deprecated.
        Description copied from interface: _PyramidServiceOperations
        Whether or not this raw pixels store requires a backing pixels pyramid to provide sub-resolutions of the data.
        Parameters:
        __cb - The callback object for the operation.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setResolutionLevel_async

        public void setResolutionLevel_async​(AMD_PyramidService_setResolutionLevel __cb,
                                     int resolutionLevel,
                                     Ice.Current __current)
                              throws ServerError
        Deprecated.
        Description copied from interface: _PyramidServiceOperations
        Sets the active resolution level.
        Parameters:
        __cb - The callback object for the operation.
        resolutionLevel - The resolution level to be used by the pixel buffer.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • getTile_async

        public void getTile_async​(AMD_RawPixelsStore_getTile __cb,
                          int z,
                          int c,
                          int t,
                          int x,
                          int y,
                          int w,
                          int h,
                          Ice.Current __current)
                   throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • setTile_async

        public void setTile_async​(AMD_RawPixelsStore_setTile __cb,
                          byte[] buf,
                          int z,
                          int c,
                          int t,
                          int x,
                          int y,
                          int w,
                          int h,
                          Ice.Current __current)
                   throws ServerError
        Deprecated.
        Description copied from interface: _RawPixelsStoreOperations
        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.
        __current - The Current object for the invocation.
        Throws:
        ServerError