exposure

exposure#

Classes:

`CTF`	CTF estimation results associated with an exposure.
`CtfStats`	CTF statistics associated with an exposure.
`Exposure`	A single exposure (movie) within a session, along with associated metadata.
`ExposureAttributes`	Exposure processing metadata.
`ExposureElement`	Outputs produced for a specific exposure.
`ExposureGroups`	Information about Outputs produced by a specific exposure
`GainRefBlob`	Metadata for gain reference blob file associated with an exposure.
`MScopeParams`	Microscope parameters associated with an exposure.
`MicrographBlob`	Metadata for motion-corrected micrograph blob file associated with an exposure.
`MotionData`	Motion correction data associated with an exposure.
`MovieBlob`	Metadata for raw movie blob file associated with an exposure.
`ParticleInfo`	Particle picking results.
`ParticleManual`	Manual particle picking results.
`PickerInfoElement`	Particle picking results for extracted particles.
`PickerLocations`	Particle picker locations stored as fractional coordinates.
`StatBlob`	Metadata for background blob .mrc file associated with an exposure.

class CTF#

CTF estimation results associated with an exposure.

Attributes:

`accel_kv`
`amp_contrast`
`cross_corr_ctffind4`
`cs_mm`
`ctf_fit_to_A`
`df1_A`
`df2_A`
`df_angle_rad`
`exp_group_id`
`fig_of_merit_gctf`
`path`
`phase_shift_rad`
`type`

accel_kv: float#

amp_contrast: float#

cross_corr_ctffind4: float#

cs_mm: float#

ctf_fit_to_A: float#

df1_A: float#

df2_A: float#

df_angle_rad: float#

exp_group_id: int#

fig_of_merit_gctf: float#

path: str#

phase_shift_rad: float#

type: str#

class CtfStats#

CTF statistics associated with an exposure.

Attributes:

`cross_corr`
`ctf_fit_to_A`
`df_range`
`df_tilt_normal`
`diag_image_path`
`fit_data_path`
`ice_thickness_rel`
`spectrum_dim`
`type`

cross_corr: int#

ctf_fit_to_A: float#

df_range: List[Any]#

df_tilt_normal: List[Any]#

diag_image_path: str#

fit_data_path: str#

ice_thickness_rel: float#

spectrum_dim: int#

type: str#

class Exposure#

A single exposure (movie) within a session, along with associated metadata.

Attributes:

`abs_file_path`	only used when first reading in this file, otherwise use `groups.exposures.movie_blob.path` relative to the project directory.
`attributes`
`created_at`	When this object was first created.
`deleted`
`discovered_at`
`ecl`
`exp_group_id`	Configured exposure group ID.
`fail_count`
`fail_reason`
`failed`
`groups`
`id`
`in_progress`
`manual_reject`
`micrograph_psize`
`micrograph_shape`
`parameter_version`
`picker_type`
`preview_img_1x`
`preview_img_2x`
`priority`
`project_uid`
`session_uid`
`size`
`stage`
`test`
`test_parameters`
`threshold_reject`
`thumb_shape`
`uid`	Unique integer identifier for this exposure within the session.
`updated_at`	When this object was last modified.
`worker_juid`

abs_file_path: str#: only used when first reading in this file, otherwise use groups.exposures.movie_blob.path relative to the project directory.

attributes: ExposureAttributes#

created_at: datetime#: When this object was first created. Imported objects such as projects and jobs will retain the created time from their original CryoSPARC instance.

deleted: bool#

discovered_at: datetime#

ecl: ECLExposureProperties#

exp_group_id: int#: Configured exposure group ID.

fail_count: int#

fail_reason: str#

failed: bool#

groups: ExposureGroups#

id: str#

in_progress: bool#

manual_reject: bool#

micrograph_psize: float | None#

micrograph_shape: List[int]#

parameter_version: int | None#

picker_type: Literal['blob', 'template', 'manual'] | None#

preview_img_1x: List[str]#

preview_img_2x: List[str]#

priority: int#

project_uid: str#

session_uid: str#

size: int#

stage: Literal['go_to_found', 'found', 'check', 'motion', 'ctf', 'thumbs', 'pick', 'extract', 'extract_manual', 'ready', 'restoring', 'restoring_motion', 'restoring_thumbs', 'restoring_ctf', 'restoring_extract', 'restoring_extract_manual', 'compacted']#

test: bool#

test_parameters: LivePreprocessingParams | None#

threshold_reject: bool#

thumb_shape: List[int]#

uid: int#: Unique integer identifier for this exposure within the session. Starts at 1 for the first found exposure and increments by 1 for each new exposure.

updated_at: datetime#: When this object was last modified.

worker_juid: str | None#

class ExposureAttributes#

Exposure processing metadata.

Attributes:

astigmatism: float#

astigmatism_angle: float#

average_defocus: float#

blob_pick_score_median: float#

check_at: float#

ctf_at: float#

ctf_fit_to_A: float#

defocus_range: float#

df_tilt_angle: float#

extract_at: float#

found_at: float#

ice_thickness_rel: float#

manual_extract_at: float#

max_intra_frame_motion: float#

motion_at: float#

phase_shift: float#

pick_at: float#

ready_at: float#

template_pick_score_median: float#

thumbs_at: float#

total_blob_picks: int#

total_extracted_particles: int#

total_extracted_particles_blob: int#

total_extracted_particles_manual: int#

total_extracted_particles_template: int#

total_manual_picks: int#

total_motion_dist: float#

total_template_picks: int#

class ExposureElement#

Outputs produced for a specific exposure.

Attributes:

`background_blob`
`ctf`
`ctf_stats`
`gain_ref_blob`
`micrograph_blob`
`micrograph_blob_non_dw`
`micrograph_blob_thumb`
`movie_blob`
`mscope_params`
`rigid_motion`
`spline_motion`
`uid`

background_blob: StatBlob | None#

ctf: CTF | None#

ctf_stats: CtfStats | None#

gain_ref_blob: GainRefBlob | None#

micrograph_blob: MicrographBlob | None#

micrograph_blob_non_dw: MicrographBlob | None#

micrograph_blob_thumb: MicrographBlob | None#

movie_blob: MovieBlob | None#

mscope_params: MScopeParams | None#

rigid_motion: MotionData | None#

spline_motion: MotionData | None#

uid: str#

class ExposureGroups#

Information about Outputs produced by a specific exposure

Attributes:

`exposure`	Exposures have an list of length 1 values for each field in each prefix below.
`particle_blob`	Blob picks have a list of fields, a count, and a path to a cs file
`particle_deep`	Unused for now :meta private:
`particle_extracted`	Starts as empty dict, but gets populated as a list of dictionaries.
`particle_manual`	Manual picks have a list of values for each field in each prefix
`particle_manual_extracted`	Starts as empty dict, but gets populated as a list of dictionaries
`particle_template`	Template picks have a list of fields, a count, and a path to a cs file

exposure: ExposureElement#: Exposures have an list of length 1 values for each field in each prefix below.

particle_blob: ParticleInfo#: Blob picks have a list of fields, a count, and a path to a cs file

particle_deep: Dict[str, Any]#: Unused for now :meta private:

particle_extracted: List[PickerInfoElement] | ParticleInfo#: Starts as empty dict, but gets populated as a list of dictionaries. Used for 2-slot extraction.

particle_manual: ParticleManual#: Manual picks have a list of values for each field in each prefix

particle_manual_extracted: PickerInfoElement#: Starts as empty dict, but gets populated as a list of dictionaries

particle_template: ParticleInfo#: Template picks have a list of fields, a count, and a path to a cs file

class GainRefBlob#

Metadata for gain reference blob file associated with an exposure.

Attributes:

`flip_x`
`flip_y`
`idx`
`path`
`rotate_num`
`shape`

flip_x: int#

flip_y: int#

idx: int#

path: str#

rotate_num: int#

shape: List[int]#

class MScopeParams#

Microscope parameters associated with an exposure.

Attributes:

`accel_kv`
`beam_shift`
`beam_shift_known`
`cs_mm`
`defect_path`
`exp_group_id`
`neg_stain`
`phase_plate`
`total_dose_e_per_A2`

accel_kv: float#

beam_shift: List[int]#

beam_shift_known: int#

cs_mm: float#

defect_path: str | None#

exp_group_id: int#

neg_stain: int#

phase_plate: int#

total_dose_e_per_A2: float#

class MicrographBlob#

Metadata for motion-corrected micrograph blob file associated with an exposure.

Attributes:

`format`
`idx`
`is_background_subtracted`
`path`
`psize_A`
`shape`

format: str#

idx: int#

is_background_subtracted: bool#

path: str#

psize_A: float#

shape: List[int]#

class MotionData#

Motion correction data associated with an exposure.

Attributes:

`frame_end`
`frame_start`
`idx`
`path`
`psize_A`
`type`
`zero_shift_frame`

frame_end: int#

frame_start: int#

idx: int#

path: str#

psize_A: float#

type: str#

zero_shift_frame: int#

class MovieBlob#

Metadata for raw movie blob file associated with an exposure.

Attributes:

`format`
`has_defect_file`
`import_sig`	Unique 64 bit import signature for this exposure, created by computing the sha1 of the original absolute path and taking the first 8 bytes.
`is_gain_corrected`
`path`
`psize_A`
`shape`

format: str#

has_defect_file: bool#

import_sig: str#

Unique 64 bit import signature for this exposure, created by computing the sha1 of the original absolute path and taking the first 8 bytes.

Encoded as a string when saved to mongo or JSON to avoid 32 bit overflow errors. When using instances of the MovieBlob model from Python, import_sig should be treated as a regular int.

is_gain_corrected: bool#

path: str#

psize_A: float#

shape: List[int]#

class ParticleInfo#

Particle picking results.

Attributes:

`count`
`fields`
`path`

count: int#

fields: List[str]#

path: str#

class ParticleManual#

Manual particle picking results.

Attributes:

`count`
`fields`
`location`
`path`

count: int#

fields: List[str]#

location: PickerLocations#

path: str#

class PickerInfoElement#

Particle picking results for extracted particles.

Attributes:

`count`
`fields`
`output_shape`
`path`
`picker_type`

count: int#

fields: List[str]#

output_shape: int | None#

path: str#

picker_type: Literal['blob', 'template', 'manual'] | None#

class PickerLocations#

Particle picker locations stored as fractional coordinates. center_x_frac and center_y_frac always have the same length.

Attributes:

`center_x_frac`
`center_y_frac`

center_x_frac: List[float]#

center_y_frac: List[float]#

class StatBlob#

Metadata for background blob .mrc file associated with an exposure.

Attributes:

`binfactor`
`idx`
`path`
`psize_A`
`shape`

binfactor: int#

idx: int#

path: str#

psize_A: float#

shape: List[int]#

`astigmatism`
`astigmatism_angle`
`average_defocus`
`blob_pick_score_median`
`check_at`
`ctf_at`
`ctf_fit_to_A`
`defocus_range`
`df_tilt_angle`
`extract_at`
`found_at`
`ice_thickness_rel`
`manual_extract_at`
`max_intra_frame_motion`
`motion_at`
`phase_shift`
`pick_at`
`ready_at`
`template_pick_score_median`
`thumbs_at`
`total_blob_picks`
`total_extracted_particles`
`total_extracted_particles_blob`
`total_extracted_particles_manual`
`total_extracted_particles_template`
`total_manual_picks`
`total_motion_dist`
`total_template_picks`

exposure

Contents

exposure#