CEED Config

The following are the configuration options provided by the app. It can be configured by changing appropriate values in the config.yaml settings file. The options default to the default value of the classes for each of the options.

external_function_plugin_package:

Default value:

''

The name of an external function plugin package that contains additional functions to be displayed in the GUI to the user. See plugin for details.

external_stage_plugin_package:

Default value:

''

The name of an external stage plugin package that contains additional stages to be displayed in the GUI to the user. See plugin for details.

inspect:

Default value:

false

Enables GUI inspection. If True, it is activated by hitting ctrl-e in the GUI.

last_directory:

Default value:

'~'

The last directory opened in the GUI.

view

LED_mode:

Default value:

RGB

The LED mode the projector will be set to during the experiment. Its value is from the led_modes.

LED_mode_idle:

Default value:

none

The LED mode the projector will be set to before/after the experiment. This is used to turn OFF the projector LEDs in between experiments so that light is not projected on the tissue while stages are designed. Its value is from the led_modes.

cam_transform:

Default value:

- - 1.0
  - 0.0
  - 0.0
  - 0.0
- - 0.0
  - 1.0
  - 0.0
  - 0.0
- - 0.0
  - 0.0
  - 1.0
  - 0.0
- - 0.0
  - 0.0
  - 0.0
  - 1.0

A 4x4 matrix that controls the rotation, offset, and scaling of the camera images relative to the projector. In the Ceed GUI, a user can transform the camera image, in addition to flip_camera until it fully aligns with the projector output. See also Camera-projector-array alignment.

current_blue:

Default value:

The current to use for the projector blue LED. Its value is between 0 to 43 amps.

current_green:

Default value:

27.74

The current to use for the projector green LED. Its value is between 0 to 43 amps.

current_red:

Default value:

42.32

The current to use for the projector red LED. Its value is between 0 to 43 amps.

experiment_uuid:

Default value:

!!binary ""

A unique uuid that is re-generated before each experiment and sent along over the corner pixel as the initial uniquely-identifying handshake-pattern. It allows us to locate this experiment in the MCS data post-hoc. See DataSerializerBase.

flip_camera:

Default value:

false

Whether to flip the camera images horizontally, around the center. See also Camera-projector-array alignment.

flip_projector:

Default value:

true

Whether to flip the projector output horizontally, around the center. See also Camera-projector-array alignment.

frame_rate:

Default value:

null

The frame-rate of the GPU that plays the experiment. This should be set to the exact refresh rate of the GPU, as can be found in e.g. the nvidia control panel. Otherwise, the experiment will be out of sync and played incorrectly. This is internally converted to a fraction (frame_rate_numerator, frame_rate_denominator), so the number must be such that it can be converted to a fraction. E.g. 119.96 or 59.94 can be represented correctly as fractions.

frame_rate_denominator:

Default value:

null

The denominator of the frame_rate fraction.

frame_rate_numerator:

Default value:

null

The numerator of the frame_rate fraction.

fullscreen:

Default value:

true

Whether the second Ceed window that runs the “real experiment” is run in fullscreen mode. In fullscreen mode the window has no borders and takes over the whole screen.

log_debug_timing:

Default value:

false

Whether to log the times that frames are drawn and rendered to a debug section in the h5 file. If True, this will additionally be logged for each displayed frame in a special section in the file.

mea_diameter:

Default value:

The diameter in pixels of the displayed electrode circles in the grid. See mea_transform also.

mea_num_cols:

Default value:

The number of electrode columns in the array. See mea_transform also.

mea_num_rows:

Default value:

The number of electrode rows in the array. See mea_transform also.

mea_pitch:

Default value:

The distance in pixels, center-to-center, between neighboring rows/columns. It is assumed that it is the same for columns and rows. See mea_transform also.

mea_transform:

Default value:

- - 1.0
  - 0.0
  - 0.0
  - 0.0
- - 0.0
  - 1.0
  - 0.0
  - 0.0
- - 0.0
  - 0.0
  - 1.0
  - 0.0
- - 0.0
  - 0.0
  - 0.0
  - 1.0

A 4x4 matrix that controls the rotation, offset, and scaling of the mea array relative to the camera. This is a grid that corresponds to the electrodes in the electrode array. In the Ceed GUI, a user can transform this grid, in addition to mirror_mea until it fully aligns with a camera image of the grid from the actual array. See also Camera-projector-array alignment and the other mea_ properties of this class.

mirror_mea:

Default value:

true

When True, the MEA grid is mirrored vertically around the center. See mea_transform also.

output_count:

Default value:

true

Whether the corner pixel is used to output frame information on the PROPixx controller IO pot as described in DataSerializerBase. If True, ceed.storage.controller.DataSerializerBase is used to set the 24 bits of the corner pixel. Otherwise, that pixel is treated like the other normal pixels.

pad_to_stage_handshake:

Default value:

true

Ad described in DataSerializerBase, Ceed sends handshaking data to the MCS system at the start of each experiment. This helps us align the Ceed and MCS data afterwards. If the root stage of the experiment is too short, it’s possible the full handshake would not be sent, preventing alignment afterwards. If pad_to_stage_handshake, then the root stage will be padded so it goes for the minimum number of clock frames required to finish the handshake, if it’s too short. The shapes will be black for those padded frames.

pre_compute_stages:

Default value:

false

Whether the stage run by the experiment should be pre-computed. See Pre-computing for details.

screen_height:

Default value:

The screen height in pixels on which the data is played. This is the full-screen height.

screen_offset_x:

Default value:

When there are multiple monitors, the monitor on which the experiment is shown in full-screen mode is controlled by the x-position of the displayed window. E.g. to show it on the right monitor of two monitors each 1920 pixel wide, and with the main monitor being on the left. Then the screen_offset_x should be set to 1920.

screen_width:

Default value:

The screen width in pixels on which the data is played. This is the full-screen width.

skip_estimated_missed_frames:

Default value:

true

Whether to drop frames to compensate when we detect that a previous frame was displayed for longer than a single GPU frame duration. Then, we may want to drop an equivalent number of frames, rather than displaying all the subsequent frames at a delay. See FrameEstimation and TeensyFrameEstimation for how we detect these long frames. Use TeensyFrameEstimation.use_teensy to control which estimator is used.

use_software_frame_rate:

Default value:

false

Depending on the CPU/GPU, the software may be unable to render faster than the GPU refresh rate. In that case, the GPU limits us to the GPU frame rate and frame_rate should be set to match the GPU refresh rate and this should be False. If the GPU isn’t forcing a frame rate. Then this should be True and frame_rate should be the desired frame rate. That will restrict us the given frame rate. However, the actual frame rate will be wildly inaccurate in this mode, so it’s only useful for testing. One can tell whether the GPU is forcing a frame rate by setting frame_rate to a large value and setting use_software_frame_rate to False and seeing what the resultant frame rate is. If it isn’t capped at some value constant, e.g. 120Hz, it means that the GPU isn’t forcing a rate.

video_mode:

Default value:

RGB

The current video mode from among the video_modes. See also Video mode.

teensy_frame_estimation

usb_product_id:

Default value:

The Teensy product ID. This is how we find the attached Teensy on the bus. If there’s more than one, this needs to be modified.

usb_vendor_id:

Default value:

The Teensy vendor ID. This is how we find the attached Teensy on the bus. If there’s more than one, this needs to be modified.

use_teensy:

Default value:

true

Whether to use the Teensy. If it’s not attached, set this to False. When False, it falls back on FrameEstimation.

frame_estimation

skip_detection_smoothing_n_frames:

Default value:

How many frames ot average to detect when a frame needs to be skipped. See class description.

serializer

clock_idx:

Default value:

The bit index to use for the clock. A number between 0-23, inclusive.

count_indices:

Default value:

- 19
- 20

A list of bit indices to use for the long counter as explained in DataSerializerBase. Each item is a number between 0-23, inclusive. Their order is the order of the counter bit pattern. The first index is for the first (least significant) bit of the counter etc. If the length of count_indices doesn’t divide counter_bit_width exactly, the ends are padded with zeros for those bits.

counter_bit_width:

Default value:

The number of bits in the long counter, as described in DataSerializerBase. Must be a multiple of 8 (to align with a byte).

projector_to_aquisition_map:

Default value:

Maps the bit indices used by Ceed to the corresponding bit indices used by MCS. It is required to be able to align the two systems. I.e. if port zero of the projector is connected to port 3 of the MCS controller, then this would be {0: 3}.

short_count_indices:

Default value:

- 3
- 4
- 10
- 11
- 12
- 18

A list of bit indices to use for the short counter as explained in DataSerializerBase. Each item is a number between 0-23, inclusive. Their order is the order of the counter bit pattern. E.g. if it was [1, 3], the the bit pattern for just the counter would look like: 0b0000, 0b0010, 0b1000, 0b1010, 0b0000, 0b0010, 0b1000…

player

player_name:

Default value:

ffmpeg

The name of the currently selected video player. It is one of “ffmpeg”, “thor”, “flir”, or “client”.

video_recorder

estimate_record_rate:

Default value:

false

Whether to use cpl_media.player.BasePlayer.real_rate for the recorder frame rate, as opposed to the one initially provided by the player.

metadata_record:

Default value:

null

(internal) Describes the video metadata of the recorder. This is the requested format, or best guess of the metadata. Read only.

record_directory:

Default value:

/home/runner

The directory into which videos should be saved.

record_fname:

Default value:

video{}.mkv

The filename to be used to record the next video. If {} is present in the filename, it’ll be replaced with the value of record_fname_count which auto increments after every video, when used. We use Python’s format machinery for this.

record_fname_count:

Default value:

A counter that auto increments by one after every recorded video. Used to give unique filenames for each video file. See record_fname.

requested_record_duration:

Default value:

The total duration that we should record. If zero, duration was not set.

thor

binning_x:

Default value:

The x binning value to use.

binning_x_range:

Default value:

- 0
- 0

The supported exposure range.

binning_y:

Default value:

The y binning value to use.

binning_y_range:

Default value:

- 0
- 0

The supported exposure range.

black_level:

Default value:

The black level value to use.

black_level_range:

Default value:

- 0
- 100

The supported exposure range.

color_gain:

Default value:

- 1
- 1
- 1

The color gain for each red, green, and blue channel.

exposure_ms:

Default value:

The exposure value in ms to use.

exposure_range:

Default value:

- 0
- 100

The supported exposure range in ms.

frame_queue_size:

Default value:

The max number of image frames to be allowed on the camera’s hardware queue. Once exceeded, the frames are dropped.

freq:

Default value:

20 MHz

The frequency to use.

gain:

Default value:

The gain value to use.

gain_range:

Default value:

- 0
- 100

The supported exposure range.

metadata_play:

Default value:

null

(internal) Describes the video metadata of the video player. This is the requested format, or best guess of the metadata. Read only.

metadata_play_used:

Default value:

null

(internal) Describes the video metadata of the video player that is actually used by the player. This must be set before recorders may allow recording the player. Depending on the metadata needed by the recorder, it may refuse to record until the needed metadata is given. Read only.

num_queued_frames:

Default value:

The number of image frames currently on the camera’s hardware queue.

roi_height:

Default value:

The height after the y start position of the ROI in pixels, to use.

roi_width:

Default value:

The width after the x start position of the ROI in pixels, to use.

roi_x:

Default value:

The x start position of the ROI in pixels.

roi_y:

Default value:

The y start position of the ROI in pixels.

sensor_size:

Default value:

- 0
- 0

The size of the sensor in pixels.

serial:

Default value:

''

The serial number of the camera that will be opened.

serials:

Default value:

[]

The list of serial numbers representing the cameras available.

supported_freqs:

Default value:

- 20 MHz

The supported frequencies.

supported_taps:

Default value:

- '1'

The supported taps.

supported_triggers:

Default value:

- SW Trigger
- HW Trigger

The trigger types supported by the camera.

supports_color:

Default value:

false

Whether the camera supports color.

taps:

Default value:

'1'

The tap to use.

trigger_count:

Default value:

The number of frames to capture in response to the trigger.

trigger_type:

Default value:

SW Trigger

The trigger type of the camera to use.

network_client

metadata_play:

Default value:

null

(internal) Describes the video metadata of the video player. This is the requested format, or best guess of the metadata. Read only.

metadata_play_used:

Default value:

null

(internal) Describes the video metadata of the video player that is actually used by the player. This must be set before recorders may allow recording the player. Depending on the metadata needed by the recorder, it may refuse to record until the needed metadata is given. Read only.

port:

Default value:

The server port that broadcasts the data.

server:

Default value:

''

The server address that broadcasts the data.

timeout:

Default value:

0.01

How long to wait before timing out when reading data before checking the queue for other requests.

image_file_recorder

compression:

Default value:

raw

Whether to compress when extension is tiff. Can be one of 'raw', 'lzw', 'zip'.

extension:

Default value:

tiff

The extension of the images being saved.

metadata_record:

Default value:

null

(internal) Describes the video metadata of the recorder. This is the requested format, or best guess of the metadata. Read only.

record_directory:

Default value:

/home/runner

The directory into which videos should be saved.

record_prefix:

Default value:

image_

The prefix to the filename of the images being saved.

requested_record_duration:

Default value:

The total duration that we should record. If zero, duration was not set.

flir

metadata_play:

Default value:

null

(internal) Describes the video metadata of the video player. This is the requested format, or best guess of the metadata. Read only.

metadata_play_used:

Default value:

null

(internal) Describes the video metadata of the video player that is actually used by the player. This must be set before recorders may allow recording the player. Depending on the metadata needed by the recorder, it may refuse to record until the needed metadata is given. Read only.

saved_nodes:

Default value:

{}

serial:

Default value:

''

The serial number of the camera to open.

ffmpeg

dshow_filename:

Default value:

''

The name of the dshow camera to open.

dshow_opt:

Default value:

''

The camera options associated with dshow_true_filename when dshow is used.

dshow_rate:

Default value:

The frame rate to request from the dshow camera.

dshow_true_filename:

Default value:

''

The real and complete filename of the direct show (webcam) device.

file_fmt:

Default value:

''

The format used to play the video. Can be empty or a format e.g. mjpeg for webcams.

icodec:

Default value:

''

The codec used to open the video stream with if it needs to be specified for the camera.

metadata_play:

Default value:

null

(internal) Describes the video metadata of the video player. This is the requested format, or best guess of the metadata. Read only.

metadata_play_used:

Default value:

null

(internal) Describes the video metadata of the video player that is actually used by the player. This must be set before recorders may allow recording the player. Depending on the metadata needed by the recorder, it may refuse to record until the needed metadata is given. Read only.

play_filename:

Default value:

''

The filename of the media being played. Can be e.g. a filename etc.

use_dshow:

Default value:

true

Whether we use dshow - i.e. USB webcams, or normal media sources.

function

data

backup_interval:

Default value:

5.0

How frequently the backup file is flushed to disk. The backup file is the one into which all new data is written to until saved explicitly in the GUI to the current data file. Until that happens, we write date to the backup file.

compression:

Default value:

Auto

Whether the h5 data file should internally compress the data that it writes. This is handled internally by the H5 library, with no external difference in how the file is loaded/saved/accessed, except that the file size may be smaller when compressed. Additionally, it may take a little more CPU when saving experiment data if compressions is enabled. Valid values are "ZIP", "None", or "Auto".

root_path:

Default value:

''

The directory part of the path where the data is saved.