pcdsdevices.areadetector.plugins.HDF5Plugin

class pcdsdevices.areadetector.plugins.HDF5Plugin(*args, **kwargs)

Ophyd Device Components
Attribute	Class	Suffix	Docs	Kind	Notes
configuration_names	`ArrayAttributeSignal`			config	Inherited from `HDF5Plugin`
array_counter (ADComponent)	`EpicsSignalWithRBV`	`ArrayCounter`	[ArrayCounter r/w longout] Counter that increments by 1 each time an NDArray callback is processed	normal	Inherited from `HDF5Plugin`
array_rate (ADComponent)	`EpicsSignalRO`	`ArrayRate_RBV`	[ArrayRate_RBV r/o calc] Rate (Hz) at which ArrayCounter is incrementing. Computed in database.	normal	Inherited from `HDF5Plugin`
asyn_io (ADComponent)	`EpicsSignal`	`AsynIO`	[AsynIO N/A asyn] asyn record to control debugging (asynTrace)	normal	Inherited from `HDF5Plugin`
nd_attributes_file (ADComponent)	`EpicsSignal`	`NDAttributesFile`	[NDAttributesFile r/w waveform] The name of an XML file defining the PVAttributes and paramAttributes to be added to each NDArray by this plugin. The format of the XML file is described in the documentation for asynNDArrayDriver::readNDAttributesFile().	normal	Inherited from `HDF5Plugin`
pool_alloc_buffers (ADComponent)	`EpicsSignalRO`	`PoolAllocBuffers`	[PoolAllocBuffers r/o longin] The number of NDArrays this plugin has currently allocated.	normal	Inherited from `HDF5Plugin`
pool_free_buffers (ADComponent)	`EpicsSignalRO`	`PoolFreeBuffers`	[PoolFreeBuffers r/o longin] The number of free NDArrays this plugin has in its NDArrayPool.	normal	Inherited from `HDF5Plugin`
pool_max_buffers (ADComponent)	`EpicsSignalRO`	`PoolMaxBuffers`	[PoolMaxBuffers r/o longin] The maximum number of NDArrays this plugin is allowed to allocate.	normal	Inherited from `HDF5Plugin`
pool_max_mem (ADComponent)	`EpicsSignalRO`	`PoolMaxMem`	[PoolMaxMem r/o ai] The maximum amount of NDArrayPool memory this plugin is allowed to allocate.	normal	Inherited from `HDF5Plugin`
pool_used_buffers (ADComponent)	`EpicsSignalRO`	`PoolUsedBuffers`	[PoolUsedBuffers N/A calc] The number of used NDArrays this plugin has in its NDArrayPool. Calculated from PoolAllocBuffers and PoolFreeBuffers.	normal	Inherited from `HDF5Plugin`
pool_used_mem (ADComponent)	`EpicsSignalRO`	`PoolUsedMem`	[PoolUsedMem r/o ai] The actual amount of NDArrayPool memory this plugin is currently using.	normal	Inherited from `HDF5Plugin`
port_name (ADComponent)	`EpicsSignalRO`	`PortName_RBV`	[PortName_RBV r/o stringin] asyn port name	config	Inherited from `HDF5Plugin`
asyn_pipeline_config	`ArrayAttributeSignal`			config	Inherited from `HDF5Plugin`
width (ADComponent)	`EpicsSignalRO`	`ArraySize0_RBV`	[ArraySize0_RBV r/o longin] First dimension of NDArray callback data	normal	Inherited from `HDF5Plugin`
height (ADComponent)	`EpicsSignalRO`	`ArraySize1_RBV`	[ArraySize1_RBV r/o longin] Second dimension of NDArray callback data	normal	Inherited from `HDF5Plugin`
depth (ADComponent)	`EpicsSignalRO`	`ArraySize2_RBV`	[ArraySize2_RBV r/o longin] Third dimension of NDArray callback data	normal	Inherited from `HDF5Plugin`
array_size (DDC)	`ArraySize`	(See below)		normal	Inherited from `HDF5Plugin`
bayer_pattern (ADComponent)	`EpicsSignalRO`	`BayerPattern_RBV`	[BayerPattern_RBV r/o mbbi] BayerPattern of last NDArray callback data (NDBayerPattern_t).	normal	Inherited from `HDF5Plugin`
blocking_callbacks (ADComponent)	`EpicsSignalWithRBV`	`BlockingCallbacks`	[BlockingCallbacks r/w bo] 0 = callbacks from the driver do not block; the NDArray data is put on a queue and the callback processes in its own thread. 1 = callbacks from the driver block; the callback processes in the driver callback thread.	config	Inherited from `HDF5Plugin`
color_mode (ADComponent)	`EpicsSignalRO`	`ColorMode_RBV`	[ColorMode_RBV r/o mbbi] Color mode of last NDArray callback data (NDColorMode_t).	normal	Inherited from `HDF5Plugin`
data_type (ADComponent)	`EpicsSignalRO`	`DataType_RBV`	[DataType_RBV r/o mbbi] Data type of last NDArray callback data (NDDataType_t).	normal	Inherited from `HDF5Plugin`
dim0_sa (ADComponent)	`EpicsSignal`	`Dim0SA`		normal	Inherited from `HDF5Plugin`
dim1_sa (ADComponent)	`EpicsSignal`	`Dim1SA`		normal	Inherited from `HDF5Plugin`
dim2_sa (ADComponent)	`EpicsSignal`	`Dim2SA`		normal	Inherited from `HDF5Plugin`
dim_sa (DDC)	`DimSa`	(See below)		normal	Inherited from `HDF5Plugin`
dimensions (ADComponent)	`EpicsSignalRO`	`Dimensions_RBV`	[Dimensions_RBV r/o waveform] Dimensions in last NDArray callback data	normal	Inherited from `HDF5Plugin`
dropped_arrays (ADComponent)	`EpicsSignalWithRBV`	`DroppedArrays`	[DroppedArrays r/w longout] Counter that increments by 1 each time an NDArray callback occurs when NDPluginDriverBlockingCallbacks=0 and the plugin driver queue is full, so the callback cannot be processed.	normal	Inherited from `HDF5Plugin`
enable (ADComponent)	`EpicsSignalWithRBV`	`EnableCallbacks`	[EnableCallbacks r/w bo] Enable (1) or disable (0) callbacks from the driver to this plugin. If callbacks are disabled then the plugin will normally be idle and consume no CPU resources.	config	Inherited from `HDF5Plugin`
min_callback_time (ADComponent)	`EpicsSignalWithRBV`	`MinCallbackTime`	[MinCallbackTime r/w ao] The minimum time in seconds between calls to processCallbacks. Any callbacks occuring before this minimum time has elapsed will be ignored. 0 means no minimum time, i.e. process all callbacks.	normal	Inherited from `HDF5Plugin`
nd_array_address (ADComponent)	`EpicsSignalWithRBV`	`NDArrayAddress`	[NDArrayAddress r/w longout] asyn port address for NDArray driver that will make callbacks to this plugin. This address can be changed at run time, connecting the plugin to a different address in the NDArray driver.	normal	Inherited from `HDF5Plugin`
nd_array_port (ADComponent)	`EpicsSignalWithRBV`	`NDArrayPort`	[NDArrayPort r/w stringout] asyn port name for NDArray driver that will make callbacks to this plugin. This port can be changed at run time, connecting the plugin to a different NDArray driver.	config	Inherited from `HDF5Plugin`
ndimensions (ADComponent)	`EpicsSignalRO`	`NDimensions_RBV`	[NDimensions_RBV r/o longin] Number of dimensions in last NDArray callback data	normal	Inherited from `HDF5Plugin`
plugin_type (ADComponent)	`EpicsSignalRO`	`PluginType_RBV`	[PluginType_RBV r/o stringin] A string describing the plugin type.	config	Inherited from `HDF5Plugin`
queue_free (ADComponent)	`EpicsSignal`	`QueueFree`	[QueueFree r/o longin] The number of free queue elements.	normal	Inherited from `HDF5Plugin`
queue_free_low (ADComponent)	`EpicsSignal`	`QueueFreeLow`		normal	Inherited from `HDF5Plugin`
queue_size (ADComponent)	`EpicsSignal`	`QueueSize`	[QueueSize r/o longin] The total queue size for callbacks when BlockingCallbacks=0.	normal	Inherited from `HDF5Plugin`
queue_use (ADComponent)	`EpicsSignal`	`QueueUse`	[QueueUse r/o calc] The number of used queue elements.	normal	Inherited from `HDF5Plugin`
queue_use_high (ADComponent)	`EpicsSignal`	`QueueUseHIGH`		normal	Inherited from `HDF5Plugin`
queue_use_hihi (ADComponent)	`EpicsSignal`	`QueueUseHIHI`		normal	Inherited from `HDF5Plugin`
time_stamp (ADComponent)	`EpicsSignalRO`	`TimeStamp_RBV`	[TimeStamp_RBV r/o ai] Time stamp number of last NDArray callback data	normal	Inherited from `HDF5Plugin`
unique_id (ADComponent)	`EpicsSignalRO`	`UniqueId_RBV`	[UniqueId_RBV r/o longin] Unique ID number of last NDArray callback data	normal	Inherited from `HDF5Plugin`
auto_increment (ADComponent)	`EpicsSignalWithRBV`	`AutoIncrement`		config	Inherited from `HDF5Plugin`
auto_save (ADComponent)	`EpicsSignalWithRBV`	`AutoSave`		config	Inherited from `HDF5Plugin`
capture (ADComponent)	`EpicsSignalWithRBV`	`Capture`		normal	Inherited from `HDF5Plugin`
delete_driver_file (ADComponent)	`EpicsSignalWithRBV`	`DeleteDriverFile`		config	Inherited from `HDF5Plugin`
file_format (ADComponent)	`EpicsSignalWithRBV`	`FileFormat`		config	Inherited from `HDF5Plugin`
file_name (ADComponent)	`EpicsSignalWithRBV`	`FileName`		config	Inherited from `HDF5Plugin`
file_number (ADComponent)	`EpicsSignalWithRBV`	`FileNumber`		normal	Inherited from `HDF5Plugin`
file_number_sync (ADComponent)	`EpicsSignal`	`FileNumber_Sync`		normal	Inherited from `HDF5Plugin`
file_number_write (ADComponent)	`EpicsSignal`	`FileNumber_write`		normal	Inherited from `HDF5Plugin`
file_path (ADComponent)	`EpicsPathSignal`	`FilePath`		config	Inherited from `HDF5Plugin`
file_path_exists (ADComponent)	`EpicsSignalRO`	`FilePathExists_RBV`		config	Inherited from `HDF5Plugin`
file_template (ADComponent)	`EpicsSignalWithRBV`	`FileTemplate`		config	Inherited from `HDF5Plugin`
file_write_mode (ADComponent)	`EpicsSignalWithRBV`	`FileWriteMode`		config	Inherited from `HDF5Plugin`
full_file_name (ADComponent)	`EpicsSignalRO`	`FullFileName_RBV`		config	Inherited from `HDF5Plugin`
num_capture (ADComponent)	`EpicsSignalWithRBV`	`NumCapture`		config	Inherited from `HDF5Plugin`
num_captured (ADComponent)	`EpicsSignalRO`	`NumCaptured_RBV`		normal	Inherited from `HDF5Plugin`
read_file (ADComponent)	`EpicsSignalWithRBV`	`ReadFile`		normal	Inherited from `HDF5Plugin`
write_file (ADComponent)	`EpicsSignalWithRBV`	`WriteFile`		normal	Inherited from `HDF5Plugin`
write_message (ADComponent)	`EpicsSignal`	`WriteMessage`		normal	Inherited from `HDF5Plugin`
write_status (ADComponent)	`EpicsSignal`	`WriteStatus`		normal	Inherited from `HDF5Plugin`
boundary_align (ADComponent)	`EpicsSignalWithRBV`	`BoundaryAlign`	[BoundaryAlign r/w longout] Set the disk boundary alignment in bytes. This parameter can be used to optimise file I/O performance on some file systems. For instance on the Lustre file system where the it is optimal to align data to the ‘stripe size’ (default 1MB). This parameter applies to all datasets in the file. Setting this parameter to 0 disables use of disk boundary alignment. Warning: setting this parameter to a larger size than the size of a single chunk will cause datafiles to grow larger than the actual contained data.	config	Inherited from `HDF5Plugin`
boundary_threshold (ADComponent)	`EpicsSignalWithRBV`	`BoundaryThreshold`	[BoundaryThreshold r/w longout] Set a minimum size (bytes) of chunk or dataset where boundary alignment is to be applied. This can be used to filter out small datasets like NDAttributes from the boundary alignment as it could blow up the file size. Setting this parameter to 0 will disable the use of boundary alignment	config	Inherited from `HDF5Plugin`
compression (ADComponent)	`EpicsSignalWithRBV`	`Compression`	[Compression r/w mbbo] Select or switch off compression filter	config	Inherited from `HDF5Plugin`
data_bits_offset (ADComponent)	`EpicsSignalWithRBV`	`DataBitsOffset`	[DataBitsOffset r/w longout] N-bit compression filter: dataword bit-offset in pixel	config	Inherited from `HDF5Plugin`
extra_dim_name (DDC)	`ExtraDimName`	(See below)		normal	Inherited from `HDF5Plugin`
extra_dim_size (DDC)	`ExtraDimSize`	(See below)		normal	Inherited from `HDF5Plugin`
io_speed (ADComponent)	`EpicsSignal`	`IOSpeed`	[IOSpeed r/o ai] Overall IO write speed in megabit per second from first frame to file closed	config	Inherited from `HDF5Plugin`
num_col_chunks (ADComponent)	`EpicsSignalWithRBV`	`NumColChunks`	[NumColChunks r/w longout] Configure HDF5 “chunking” to approriate size for the filesystem: sets number of columns to use per chunk	config	Inherited from `HDF5Plugin`
num_data_bits (ADComponent)	`EpicsSignalWithRBV`	`NumDataBits`	[NumDataBits r/w longout] N-bit compression filter: number of data bits per pixel	config	Inherited from `HDF5Plugin`
num_extra_dims (ADComponent)	`EpicsSignalWithRBV`	`NumExtraDims`	[NumExtraDims r/w mbbo] Number of extra dimensions [0..2]	config	Inherited from `HDF5Plugin`
num_frames_chunks (ADComponent)	`EpicsSignalWithRBV`	`NumFramesChunks`	[NumFramesChunks r/w longout] Configure HDF5 “chunking” to approriate size for the filesystem: sets number of frames to use per chunk. For a 2D image, setting this parameter > 1 essentially implies using in-memory cache as HDF5 only writes full chunks to disk.	config	Inherited from `HDF5Plugin`
num_frames_flush (ADComponent)	`EpicsSignalWithRBV`	`NumFramesFlush`	[NumFramesFlush r/w longout] Flush the file metadata to disk every N’th frame. Image data is written to disk on every write operation, but HDF5 internal metadata to describe the data layout and indices is normally only written at close time.	config	Inherited from `HDF5Plugin`
num_row_chunks (ADComponent)	`EpicsSignalWithRBV`	`NumRowChunks`	[NumRowChunks r/w longout] Configure HDF5 “chunking” to approriate size for the filesystem: sets number of rows to use per chunk	config	Inherited from `HDF5Plugin`
run_time (ADComponent)	`EpicsSignal`	`RunTime`		config	Inherited from `HDF5Plugin`
szip_num_pixels (ADComponent)	`EpicsSignalWithRBV`	`SZipNumPixels`	[SZipNumPixels r/w longout] szip compression filter: number of pixels in filter [1..32]	config	Inherited from `HDF5Plugin`
store_attr (ADComponent)	`EpicsSignalWithRBV`	`StoreAttr`	0=’No’ 1=’Yes’	config	Inherited from `HDF5Plugin`
store_perform (ADComponent)	`EpicsSignalWithRBV`	`StorePerform`	0=’No’ 1=’Yes’	config	Inherited from `HDF5Plugin`
zlevel (ADComponent)	`EpicsSignalWithRBV`	`ZLevel`	[ZLevel r/w longout] zlib compression filter: compression level [1..9]	config	Inherited from `HDF5Plugin`

HDF5Plugin.array_size (DDC) Dynamic Device Components
Attribute	Class	Suffix	Kind	Notes
depth	`EpicsSignalRO`	`ArraySize2_RBV`	config	Inherited from `HDF5Plugin`
height	`EpicsSignalRO`	`ArraySize1_RBV`	config	Inherited from `HDF5Plugin`
width	`EpicsSignalRO`	`ArraySize0_RBV`	config	Inherited from `HDF5Plugin`

HDF5Plugin.dim_sa (DDC) Dynamic Device Components
Attribute	Class	Suffix	Kind
dim0	`EpicsSignal`	`Dim0SA`	config
dim1	`EpicsSignal`	`Dim1SA`	config
dim2	`EpicsSignal`	`Dim2SA`	config

HDF5Plugin.extra_dim_name (DDC) Dynamic Device Components
Attribute	Class	Suffix	Kind
name_x	`EpicsSignalRO`	`ExtraDimNameX_RBV`	config
name_y	`EpicsSignalRO`	`ExtraDimNameY_RBV`	config
name_n	`EpicsSignalRO`	`ExtraDimNameN_RBV`	config

HDF5Plugin.extra_dim_size (DDC) Dynamic Device Components
Attribute	Class	Suffix	Kind
size_x	`EpicsSignalWithRBV`	`ExtraDimSizeX`	config
size_y	`EpicsSignalWithRBV`	`ExtraDimSizeY`	config
size_n	`EpicsSignalWithRBV`	`ExtraDimSizeN`	config

Methods

configure(d: Dict[str, Any]) → Tuple[Dict[str, Any], Dict[str, Any]]

Configure the device for something during a run

This default implementation allows the user to change any of the configuration_attrs. Subclasses might override this to perform additional input validation, cleanup, etc.

Parameters:

d (dict) – The configuration dictionary. To specify the order that the changes should be made, use an OrderedDict.

Returns:

(old, new) tuple of dictionaries
Where old and new are pre- and post-configure configuration states.

describe() → OrderedDictType[str, Dict[str, Any]]

Provide schema and meta-data for read().

This keys in the OrderedDict this method returns must match the keys in the OrderedDict return by read().

This provides schema related information, (ex shape, dtype), the source (ex PV name), and if available, units, limits, precision etc.

Returns:: data_keys (OrderedDict) – The keys must be strings and the values must be dict-like with the event_model.event_descriptor.data_key schema.

disable_on_stage()

when the plugin is staged, ensure that it is disabled.

a convenience method for adding `('enable', 0) to stage_sigs

enable_on_stage()

when the plugin is staged, ensure that it is enabled.

a convenience method for adding (‘enable’, 1) to stage_sigs

ensure_blocking()

Ensure that if plugin is enabled after staging, callbacks block.

a convenience method for adding `('blocking_callbacks', 1) to stage_sigs

ensure_nonblocking()

Ensure that if plugin is enabled after staging, callbacks don’t block.

a convenience method for adding `('blocking_callbacks', 0) to stage_sigs

find_signal(text, use_re=False, case_sensitive=False, match_fcn=None, f=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Search through the signal docs on this detector for the string text

Parameters:

text (str) – Text to find
use_re (bool, optional) – Use regular expressions
case_sensitive (bool, optional) – Case sensitive search
match_fcn (callable, optional) – Function to call when matches are found Defaults to a function that prints matches to f
f (file-like, optional) – File-like object that the default match function prints to (Defaults to sys.stdout)

generate_datum(key, timestamp, datum_kwargs)

get(**kwargs)

Get the value of all components in the device

Keyword arguments are passed onto each signal.get(). Components beginning with an underscore will not be included.

get_asyn_digraph()

Get the directed graph of the ASYN ports

Returns:

G (networkx.DiGraph) – Directed graph of pipelines
port_map (dict) – Mapping between port_name and ADBase objects

get_asyn_port_dictionary()

Return port name : component map

Returns:: port_map (dict) – Mapping between port_name and ADBase objects

get_plugin_by_asyn_port(port_name)

Get the plugin which has the given asyn port name

Parameters:: port_name (str) – The port name to search for
Returns:: ret (ADBase or None) – Either the requested plugin or None if not found

missing_plugins(): Find missing ports

read() → OrderedDictType[str, Dict[str, Any]]

Read data from the device.

This method is expected to be as instantaneous as possible, with any substantial acquisition time taken care of in trigger().

The OrderedDict returned by this method must have identical keys (in the same order) as the OrderedDict returned by describe().

By convention, the first key in the return is the ‘primary’ key and maybe used by heuristics in bluesky.

The values in the ordered dictionary must be dict (-likes) with the keys {'value', 'timestamp'}. The 'value' may have any type, the timestamp must be a float UNIX epoch timestamp in UTC.

Returns:: data (OrderedDict) – The keys must be strings and the values must be dict-like with the keys {'value', 'timestamp'}

read_configuration()

Dictionary mapping names to value dicts with keys: value, timestamp

To control which fields are included, change the Component kinds on the device, or modify the configuration_attrs list.

stop(*, success=False): Stop the Device and all (instantiated) subdevices

summary()

trigger() → StatusBase

Trigger the device and return status object.

This method is responsible for implementing ‘trigger’ or ‘acquire’ functionality of this device.

If there is an appreciable time between triggering the device and it being able to be read (via the read() method) then this method is also responsible for arranging that the StatusBase object returned by this method is notified when the device is ready to be read.

If there is no delay between triggering and being readable, then this method must return a StatusBase object which is already completed.

Returns:: status (StatusBase) – StatusBase object which will be marked as complete when the device is ready to be read.

validate_asyn_ports()

Validate that all components of pipeline are known

Raises:: RuntimeError – If there any input ports to known plugins where the source is not known to ophyd

visualize_asyn_digraph(ax=None, *args, **kwargs)

This generates a figure showing the current asyn port layout.

This method generates a plot showing all of the currently enabled Areadetector plugin asyn ports and their relationships. The current ports and relationships are found using self.get_asyn_digraph.

Parameters:

ax (matplotlib axes) – if None (default) then a new figure is created otherwise it is plotted on the specified axes.
*args (networkx.draw_networkx args and kwargs.) – For the allowed args and kwargs see the networkx.draw_networkx documentation
**kwargs (networkx.draw_networkx args and kwargs.) –
For the allowed args and kwargs see the networkx.draw_networkx documentation

warmup()

A convenience method for ‘priming’ the plugin.

The plugin has to ‘see’ one acquisition before it is ready to capture. This sets the array size, etc.

Attributes

ad_root

array_pixels: The total number of pixels, calculated from array_size.

configuration_attrs

connected

hints

kind

source_plugin

subscriptions: ClassVar[FrozenSet[str]] = frozenset({'acq_done'})