pyfast_adt.main.adaptor.camera.generalized_adapcam_to_edit

Attributes

`type_dict`
`cam`

Classes

Cam_xf416r

Software interface for the EMMENU program and camc5.22 to control live readout of the buffer for acquiring series

Functions

EMVector2dict(vec)

Convert EMVector object to a Python dictionary.

Module Contents

pyfast_adt.main.adaptor.camera.generalized_adapcam_to_edit.type_dict

pyfast_adt.main.adaptor.camera.generalized_adapcam_to_edit.EMVector2dict(vec): Convert EMVector object to a Python dictionary.

class pyfast_adt.main.adaptor.camera.generalized_adapcam_to_edit.Cam_xf416r(drc_name: str = 'Diffraction', name: str = 'emmenu')

Bases: pyfast_adt.main.adaptor.camera.adaptor_cam.Cam_base

Software interface for the EMMENU program and camc5.22 to control live readout of the buffer for acquiring series of images Communicates with EMMENU over the COM interface defined by TVIPS, and directly to the camera using the API of TVIPS. EMMENU is used to give a friendly way to set up the camera parameters and see the live view of the camera. TVIPS API is used to acquire the images from the camera buffer, to reach 20 FPS during acquisition. its required to have a folder tree in EMMENU called Diffraction drc_name : str Set the default folder to store data in name : str Name of the interface

name = 'emmenu'

exposure = None

x = None

y = None

processing = None

delay = None

binning = None

buffer_size = None

stop_signal = None

_memReader

image = None

result_param = []

_obj

_recording = False

_cam

_vp

_immgr

_emf

_emi

top_drc_index

top_drc_name

drc_name = 'Diffraction'

drc_index

streamable = False

default_exposure = 50

default_binsize = 4

dimensions = 1024

CAMCLIB

cameraGPU

cameraLiveGPU

release_connection(): ‘ release the connection with the device

set_exposure(exposure_time: int): ‘ set the exposure time in ms for the camera

get_exposure(): ‘ get the exposure time in ms for the camera

start_liveview(delay: float): ‘ start the live view of the camera

stop_liveview(): ‘ stop the live view of the camera

set_binning(binning: int): ‘ set the binning of the camera, common parameters are 1, 2, 4, 8

get_binning(): ‘ get the binning of the camera

acquire_image(exposure_time: int, binning: int, processing: str): Acquire image through its adaptor and return it as np.array.

set_processing(processing: str): ‘ set the processing of the camera, processing = “Unprocessed, Background subtracted, Gain normalized”

get_processing(): ‘ get the processing typeof the camera

acquire_series_images(exposure_time: int, binning: int, processing: str, buffer_size: int, stop_signal)

listConfigs() → list: List the configs from the Configuration Manager.

getCurrentConfigName() → str: Return the name of the currently selected configuration in EMMENU.

getCurrentConfig(as_dict: bool = True) → dict: Get selected config object currently associated with the viewport.

getCurrentCameraInfo() → dict: Gets the current camera object.

getCameraType() → str: Get the name of the camera currently in use.

getEMMenuVersion() → str: Get the version number of EMMENU.

lock() → None

Lockdown interactions with emmenu, must call self.unlock to unlock.

If EMMenu is locked, no mouse or keyboard input will be accepted by the interface. The script calling this function is responsible for unlocking EMMenu.

unlock() → None: Unlock emmenu after it has been locked down with self.lock

listDirectories() → dict: List subdirectories of the top directory.

getEMVectorByIndex(img_index: int, drc_index: int = None) → dict: Returns the EMVector by index as a python dictionary.

deleteAllImages() → None: Clears all images currently stored in EMMENU buffers.

deleteImageByIndex(img_index: int, drc_index: int = None) → int: Delete the image from EMMENU by its index.

getImageByIndex(img_index: int, drc_index: int = None) → int

Grab data from the image manager by index. Return image pointer (COM).

Not accessible through server.

getImageDataByIndex(img_index: int, drc_index: int = None) → numpy.array

Grab data from the image manager by index.

Return numpy 2D array

getCameraDimensions(): Get the maximum dimensions reported by the camera.

getImageDimensions(): Get the dimensions of the image.

getPhysicalPixelsize(): Returns the physical pixel size of the camera nanometers.

getBinning() → int: Returns the binning corresponding to the currently selected camera config.

getCameraName() → str: Get the name reported by the camera.

writeTiffFromPointer(image_pointer, filename: str) → None: Write tiff file using the EMMENU machinery image_pointer is the memory address returned by getImageIndex()

writeTiff(image_index, filename: str) → None: Write tiff file using the EMMENU machinery image_index is the index in the current directory of the image to be written.

writeTiffs(start_index: int, stop_index: int, path: str, clear_buffer: bool = False) → None: Write a series of data in tiff format and writes them to the given path using EMMENU machinery.

getImage(**kwargs) → numpy.array: Acquire image through EMMENU and return data as np array.

acquireImage(**kwargs) → int: Acquire image through EMMENU and store in the Image Manager Returns the image index.

set_image_index(index: int) → None: Change the currently selected buffer by the image index Note that the interface here is 0-indexed, whereas the image manager is 1-indexed (FIXME)

get_image_index() → int: Retrieve the index of the currently selected buffer, 0-indexed.

get_next_empty_image_index() → int: Get the next empty buffer in the image manager, 0-indexed.

stop_record() → int

start_record() → int

set_autoincrement(toggle: bool) → None: Tell EMMENU to autoincrement the index number (True/False)

get_timestamps(start_index: int, end_index: int) → list: Get timestamps in seconds for given image index range.

releaseConnection() → None: Release the connection to the camera.

GetCurrentCameraConfiguration() → tvips.common.types.CameraConfiguration

_readSingleImage(cameraFormat: tvips.common.types.CameraFormat)

prepare_acquisition_cRED_data(camera, binning, exposure, buffer_size): “ camera = XF416 or XF416R, binning = one of the available binning for the choosen camera, exposure = choosen exposure, buffer_size = dimension of the stack where saving the output images

acquisition_cRED_data(stage_thread=None): Acquire images into the buffer up to the thread is alive, usually the stage thread is passed for cRED experiments

save_cRED_data(savingpath)

get_camera_characteristic()

load_calibration_table(path)

pyfast_adt.main.adaptor.camera.generalized_adapcam_to_edit.cam