### Install crYOLO Dependencies

Source: https://tools.cryosparc.com/_sources/intro.md

Installs additional dependencies required for the crYOLO example notebooks, including PyQt5, libtiff, wxPython, and cryolo.

```sh
conda install -c conda-forge pyqt=5 libtiff wxPython=4.1.1 adwaita-icon-theme 'setuptools<66'
pip install 'cryolo[c11]' --extra-index-url https://pypi.ngc.nvidia.com
```

--------------------------------

### start

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Builds and starts a CryoSPARC Live Session, including engines and workers based on session and lane parameters.

```APIDOC
## start

### Description
Builds and starts a CryoSPARC Live Session. Builds file engines based on file engine parameters in the session doc, builds phase one workers based on lane parameters in the session doc.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”
- **session_uid** (str) - Session UID, e.g., “S3”

### Returns
Successful Response

Return type:
Session
```

--------------------------------

### Install cryosparc-tools

Source: https://tools.cryosparc.com/_sources/intro.md

Install the latest version of cryosparc-tools from PyPI into your current Python environment.

```sh
pip install cryosparc-tools
```

--------------------------------

### Create and Activate Conda Environment for Examples

Source: https://tools.cryosparc.com/

Create a new Conda environment named 'cryosparc-tools-example' with specified Python and NumPy versions, and then activate it. This environment is recommended for running the example Jupyter notebooks.

```bash
conda create -n cryosparc-tools-example -c conda-forge python=3 numpy==1.18.5
conda activate cryosparc-tools-example
```

--------------------------------

### CryoSPARC Connection Setup

Source: https://tools.cryosparc.com/examples/live-session.html

Define the master hostname and port for your CryoSPARC installation and establish a connection using the cryosparc.tools library. Ensure the hostname and port match your login token.

```python
master_hostname = "localhost"  # should match hostname portion of login token
base_port = 62000  # should match port portion of login token

import time

import cryosparc.tools

cs = cryosparc.tools.CryoSPARC(f"http://{master_hostname}:{base_port}")
assert cs.test_connection()
api = cs.api

```

--------------------------------

### start_session

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Builds and starts a CryoSPARC Live Session.

```APIDOC
## start_session

### Description
Builds and starts a CryoSPARC Live Session.

### Parameters
- **project_uid**: The unique identifier for the project.
- **session_uid**: The unique identifier for the session.

### Usage
`start(project_uid, session_uid, /)`
```

--------------------------------

### start

Source: https://tools.cryosparc.com/api/cryosparc.controllers.job.html

Set the job status to 'running' or 'waiting'.

```APIDOC
## start

### Description
Set job status to “running” or “waiting”.

### Parameters
#### Parameters
- **status** (str) - Optional - "running" or "waiting". Defaults to "waiting".
```

--------------------------------

### Dynamic Slot Specification Example

Source: https://tools.cryosparc.com/api/cryosparc.spec.html

This example demonstrates how to specify slots with dynamic names, such as the 'components_mode_X' outputs from a 3D Variability job. The 'required' key is only applicable to input slots.

```python
[
    "blob",
    "?locations",
    {"name": "components_mode_0", "dtype": "components"},
    {"name": "components_mode_1", "dtype": "components", "required": False},
    {"name": "components_mode_2", "dtype": "components", "required": False},
]

```

--------------------------------

### Incorrect Usage Examples for api.assets.upload

Source: https://tools.cryosparc.com/api/cryosparc.api.html

These examples demonstrate incorrect ways to call the api.assets.upload function, which will result in a TypeError. Ensure all required arguments are provided correctly.

```python
api.assets.upload('P3', 'J42', my_stream, 'output.txt', 'txt')
```

```python
api.assets.upload('P3', job_uid='J42', stream=my_stream, filename='output.txt', format='txt')
```

```python
api.assets.upload(project_uid='P3', job_uid='J42', stream=my_stream, filename='output.txt', format='txt')
```

--------------------------------

### Update Session Parameters and Start Session

Source: https://tools.cryosparc.com/examples/live-session.html

Updates the overall session parameters and then starts the live session. This is a prerequisite for initiating any processing jobs.

```python
api.sessions.update_session_params(project_uid, session_uid, session_params)

api.sessions.start(project_uid, session_uid)
```

--------------------------------

### run

Source: https://tools.cryosparc.com/api/cryosparc.controllers.job.html

Starts a job within a context manager and stops it when the context ends.

```APIDOC
## run

### Description
Start a job within a context manager and stop the job when the context ends.

### Method
run

### Yields
_ExternalJob_ – self.

### Examples
Job will be marked as “failed” if the contents of the block throw an exception
```python
>>> with job.run():
...     job.save_output(...) 
```
```

--------------------------------

### register

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Registers a user with a token, typically for initial setup.

```APIDOC
## register

### Description
Registers a user using a provided token. This is typically an unauthenticated operation used for initial user setup.

### Method
POST

### Endpoint
/register

### Parameters
#### Request Body
- **user_id** (str) - Required - The User ID or Email Address for the new registration.
- **body** (SHA256Password) - Required - The SHA256 hashed password for the user.
- **token** (str) - Required - The registration token.

### Request Example
```json
{
  "user_id": "user_to_register@example.com",
  "body": "a1b2c3d4e5f6...",
  "token": "valid_registration_token"
}
```

### Returns
#### Success Response (200)
- No content is returned upon successful registration.
```

--------------------------------

### Install Specific cryosparc-tools Version

Source: https://tools.cryosparc.com/

Install a specific minor version of cryosparc-tools that corresponds to your CryoSPARC minor release version. For example, to install for CryoSPARC v4.1, use `pip install cryosparc-tools~=4.1.0`.

```bash
pip install cryosparc-tools~=4.1.0

```

--------------------------------

### setup_phase2_abinit

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up an Ab-Initio Reconstruction job for a session.

```APIDOC
## setup_phase2_abinit

### Description
Sets up an Ab-Initio Reconstruction job for a session.

### Parameters
- **project_uid**: The unique identifier for the project.
- **session_uid**: The unique identifier for the session.

### Usage
`setup_phase2_abinit(project_uid, session_uid, /)`
```

--------------------------------

### setup_phase2_abinit

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up an Ab-Initio Reconstruction job for a session.

```APIDOC
## setup_phase2_abinit

### Description
Setup Ab-Initio Reconstruction job for a session.

### Parameters
- **project_uid** (str) - Project UID, e.g., “P3”
- **session_uid** (str) - Session UID, e.g., “S3”

### Returns
Job
```

--------------------------------

### Install specific cryosparc-tools version

Source: https://tools.cryosparc.com/_sources/intro.md

Install a specific minor release version of cryosparc-tools that corresponds to your CryoSPARC minor release version. For example, for CryoSPARC v4.1.2, use `pip install cryosparc-tools~=4.1.0`.

```sh
pip install cryosparc-tools~=4.1.0
```

--------------------------------

### start_and_migrate

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Initializes CryoSPARC and performs database migrations.

```APIDOC
## start_and_migrate

### Description
Starts up CryoSPARC for the first time and performs necessary database migrations.

### Parameters
- **license_id** (str) - Required - The license ID for CryoSPARC.

### Returns
- **None** - Indicates successful completion.
```

--------------------------------

### Install CryoSPARC Tools and Dependencies

Source: https://tools.cryosparc.com/

Install the cryoSPARC-tools package along with Matplotlib and Pandas within the activated Conda environment. These are required for running the example notebooks.

```bash
pip install matplotlib~=3.4.0 pandas==1.1.4 cryosparc-tools
```

--------------------------------

### setup_phase2_refine

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up a streaming Homogenous Refinement job for a session.

```APIDOC
## setup_phase2_refine

### Description
Sets up a streaming Homogenous Refinement job for a session.

### Parameters
- **project_uid**: The unique identifier for the project.
- **session_uid**: The unique identifier for the session.

### Usage
`setup_phase2_refine(project_uid, session_uid, /)`
```

--------------------------------

### Create and Activate Conda Environment for Examples

Source: https://tools.cryosparc.com/_sources/intro.md

Sets up a new Conda environment named 'cryosparc-tools-example' with specified Python, NumPy, Matplotlib, Pandas, and cryoSPARC-tools versions.

```sh
conda create -n cryosparc-tools-example -c conda-forge python=3 numpy==1.18.5
conda activate cryosparc-tools-example
pip install matplotlib~=3.4.0 pandas==1.1.4 cryosparc-tools
```

--------------------------------

### query_mask

Source: https://tools.cryosparc.com/api/cryosparc.dataset.html

Get a boolean array representing the items to keep in the dataset that match the given query filter. See `query` method for example query format.

```APIDOC
## query_mask(_query : Dict[str, ArrayLike]_, _invert =False_) → NDArray[bool]

### Description
Get a boolean array representing the items to keep in the dataset that match the given query filter. See `query` method for example query format.

### Parameters
#### Query
- **query** (_dict_[_str_,_ArrayLike_]) – Query description
- **invert** (_bool_, optional) – If True, returns mask with all items negated. Defaults to False.

### Returns
Query mask, may be used with the `mask()` method.

### Return type
NDArray[bool]
```

--------------------------------

### Stream Initialization Examples

Source: https://tools.cryosparc.com/api/cryosparc.stream.html

Illustrates different ways to initialize a `Stream` object, accepting various input types such as file streams, iterators, async iterators, and async readable streams.

```python
Stream(_* , _stream : IO[bytes] = None_, _media_type : str | None = None_)
```

```python
Stream(_*_ , _iterator : Iterator[bytes] = None_, _media_type : str | None = None_)
```

```python
Stream(_*_ , _astream : AsyncReadable = None_, _media_type : str | None = None_)
```

```python
Stream(_*_ , _aiterator : AsyncBinaryIterator = None_, _media_type : str | None = None_)
```

--------------------------------

### Show CLI Help

Source: https://tools.cryosparc.com/_sources/guides/cli.md

Run with the `--help` flag to see available commands and options for the cryosparc-tools CLI.

```bash
python -m cryosparc.tools --help
```

--------------------------------

### Get Active Licenses Count

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets the number of acquired licenses for running jobs.

```APIDOC
## get_active_licenses_count

### Description
Gets number of acquired licenses for running jobs 

### Returns
Successful Response 

### Return Type
int
```

--------------------------------

### setup_phase2_refine

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up a phase 2 refinement job for a given project and session.

```APIDOC
## setup_phase2_refine

### Description
Sets up a phase 2 refinement job for a given project and session.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”
- **session_uid** (str) - Session UID, e.g., “S3”

### Returns
Successful Response

Return type:
Job
```

--------------------------------

### Instance API: Get Runtime Diagnostics

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets runtime diagnostics for the CryoSPARC instance.

```APIDOC
## Get Runtime Diagnostics

### Description
Gets runtime diagnostics for the CryoSPARC instance.

### Returns
Runtime diagnostic information.
```

--------------------------------

### Instance API: Get Service Log

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets CryoSPARC service logs, filterable by date.

```APIDOC
## Get Service Log

### Description
Gets CryoSPARC service logs, filterable by date.

### Parameters
#### Path Parameters
- **service** (str) - Required - The name of the service to get logs for.
#### Query Parameters
- **days** (int) - Optional - Number of past days to retrieve logs for.
- **date** (str) - Optional - Specific date to retrieve logs for (format YYYY-MM-DD).

### Returns
Service logs.
```

--------------------------------

### Instance API: Get Update Tag

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets information about updating to the next CryoSPARC version, if one is available.

```APIDOC
## Get Update Tag

### Description
Gets information about updating to the next CryoSPARC version, if one is available.

### Returns
Update information.
```

--------------------------------

### Install Jupyter Notebook

Source: https://tools.cryosparc.com/_sources/intro.md

Command to install the Jupyter Notebook package using pip. This is required for running interactive Python sessions.

```sh
pip install notebook
```

--------------------------------

### setup_template_creation_class2D

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up a template creation class2D job for a session.

```APIDOC
## setup_template_creation_class2D

### Description
Sets up a template creation class2D job for a session.

### Parameters
- **project_uid**: The unique identifier for the project.
- **...**: Additional parameters are accepted but not specified.

### Usage
`setup_template_creation_class2D(project_uid, ...)`
```

--------------------------------

### Start External Job

Source: https://tools.cryosparc.com/examples/cryolo.html

Start the created external job to begin processing and writing outputs to the job log. This action sets the job status to 'Waiting'.

```python
job.start()

```

--------------------------------

### setup_phase2_class2D

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up a streaming 2D classification job for a session.

```APIDOC
## setup_phase2_class2D

### Description
Sets up a streaming 2D classification job for a session.

### Parameters
- **project_uid**: The unique identifier for the project.
- **session_uid**: The unique identifier for the session.

### Usage
`setup_phase2_class2D(project_uid, session_uid, /)`
```

--------------------------------

### setup_phase2_class2D

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up a streaming 2D classification job for a session.

```APIDOC
## setup_phase2_class2D

### Description
Setup streaming 2D classification job for a session.

### Parameters
- **project_uid** (str) - Project UID, e.g., “P3”
- **session_uid** (str) - Session UID, e.g., “S3”
```

--------------------------------

### Initialize CryoSPARC Connection

Source: https://tools.cryosparc.com/examples/3dflex-custom-latent-trajectory.html

Establishes a connection to the CryoSPARC instance using credentials from 'instance-info.json'. Ensure the instance-info.json file is correctly configured.

```python
import json
from pathlib import Path

import numpy as n

from cryosparc.tools import CryoSPARC

with open(Path("~", "instance-info.json").expanduser(), "r") as f:
    credentials = json.load(f)

cs = CryoSPARC(**credentials)
assert cs.test_connection()
```

--------------------------------

### setup_template_creation_class2D

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Sets up a template creation class2D job for a session, with options for picker type and particle diameter.

```APIDOC
## setup_template_creation_class2D

### Description
Setup template creation class2D job for a session.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”
- **session_uid** (str) - Session UID, e.g., “S3”
- **num_classes** (int)
- **picker_type** (Literal['blob', 'template', 'manual'])
- **num_mics** (int)
- **override_particle_diameter_A** (float | None) - Optional. Defaults to None
- **uid_lte** (int | None) - Optional. Defaults to None

### Returns
Successful Response

Return type:
Job
```

--------------------------------

### get_chain

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Finds the chain of jobs between a specified start and end job UID within a project. A job chain represents the intersection of the start job's descendants and the end job's ancestors.

```APIDOC
## get_chain(_project_uid : str_, _start_job_uid : str_, _end_job_uid : str_)

### Description
Finds the chain of jobs between start job to end job. A job chain is the intersection of the start job’s descendants and the end job’s ancestors.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”
- **start_job_uid** (str) - The UID of the starting job.
- **end_job_uid** (str) - The UID of the ending job.

### Returns
Successful Response

### Return type
List[str]
```

--------------------------------

### create

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Creates a new project.

```APIDOC
## create

### Description
Creates a new project, project directory and creates a new document in the project collection.

### Parameters
* **title** (str) - The title of the new project.
* **description** (str | None, optional) - Defaults to None.
* **parent_dir** (str) - The parent directory for the new project.

### Returns
Successful Response

### Return type
Project
```

--------------------------------

### get_session_base_params

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets base session parameters.

```APIDOC
## get_session_base_params

### Description
Gets base session parameters.

### Usage
`get_session_base_params()`
```

--------------------------------

### Create and Queue a 3-Class Ab-Initio Job

Source: https://tools.cryosparc.com/api/cryosparc.controllers.job.html

Illustrates the creation of a new 3-class ab-initio job, connecting it to existing particles, setting parameters, and then queuing it.

```python
>>> job = cs.create_job("P3", "W1", "homo_abinit"
...     connections={"particles": ("J20", "particles_selected")}
...     params={"abinit_K": 3}
... )
>>> job.queue()
>>> job.status
"queued"
```

--------------------------------

### get_configuration_profiles

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets all session configuration profiles.

```APIDOC
## get_configuration_profiles

### Description
Gets all session configuration profiles.

### Usage
`get_configuration_profiles()`
```

--------------------------------

### Initialize a Dataset

Source: https://tools.cryosparc.com/api/cryosparc.dataset.html

Create a new dataset by providing data as a list of tuples, where each tuple represents a column. The 'uid' field is automatically added.

```python
>>> dset = Dataset([
...     ("uid", [1, 2, 3]),
...     ("dat1", ["Hello", "World", "!"]),
...     ("dat2", [3.14, 2.71, 1.61])
... ])
>>> dset.descr()
[('uid', '<u8'), ('dat1', '|O'), ('dat2', '<f8')]
```

--------------------------------

### get_status

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets the status of a specific job.

```APIDOC
## get_status

### Description
Gets the status of a job.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required - The unique identifier for the project.
- **job_uid** (str) - Required - The unique identifier for the job.
```

--------------------------------

### get_categories

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets job types categorized.

```APIDOC
## get_categories

### Description
Gets job types by category.
```

--------------------------------

### Start _ab initio_ 3D Reconstruction

Source: https://tools.cryosparc.com/examples/live-session.html

Sets up, enqueues, and waits for the completion of an _ab initio_ 3D reconstruction job. This requires updated parameters and a selected input volume.

```python
api.sessions.update_phase2_abinit_params(project_uid, session_uid, abinit_params)
abinit_job_uid = api.sessions.setup_phase2_abinit(project_uid, session_uid).uid
api.sessions.enqueue_phase2_abinit(project_uid, session_uid)
cs.find_job(project_uid, abinit_job_uid).wait_for_status("completed")
```

--------------------------------

### delete

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Starts the project deletion task.

```APIDOC
## delete

### Description
Starts project deletion task. Will delete the project, its full directory, and all associated workspaces, sessions, jobs and results.

### Parameters
* **project_uid** (str) - Project UID, e.g., “P3”

### Returns
None
```

--------------------------------

### Create crYOLO Working Directories

Source: https://tools.cryosparc.com/examples/cryolo.html

Initializes the necessary subfolders within the job directory for crYOLO processing.

```python
job.mkdir("full_data")
job.mkdir("train_image")
job.mkdir("train_annot")
```

--------------------------------

### ProjectsAPI.delete

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Starts project deletion task.

```APIDOC
## ProjectsAPI.delete

### Description
Starts project deletion task.

### Parameters
- **project_uid** (str)

```

--------------------------------

### Upload Asset with Keyword Arguments

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Demonstrates correct usage of the 'upload' function, specifying keyword-only arguments for clarity and robustness. Ensure all required positional arguments are provided.

```python
api.assets.upload('P3', 'J42', my_stream, filename='output.txt', format='txt')
```

--------------------------------

### mkdir

Source: https://tools.cryosparc.com/api/cryosparc.tools.html

Create a directory in the given project.

```APIDOC
## mkdir(project_uid, target_path[, parents, ...])

### Description
Create a directory in the given project.

### Parameters
- **project_uid** (str) - The UID of the project.
- **target_path** (str) - The path of the directory to create.
- **parents** (bool, optional) - Whether to create parent directories if they don't exist.
```

--------------------------------

### Save Custom Latent Components Setup

Source: https://tools.cryosparc.com/examples/3dflex-custom-latent-trajectory.html

This is a comment indicating the setup for an external job to save custom latent components. It highlights that each component has 'components_mode_n/component' and 'components_mode_n/value' fields. Connecting to a train job ensures that output fields are passed through correctly.

```python
# each component has a components_mode_n/component and components_mode_n/value field,

```

--------------------------------

### get_symlinks

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets all symbolic links in the project directory.

```APIDOC
## get_symlinks(project_uid: str)

### Description
Gets all symbolic links in the project directory.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”

### Returns
Successful Response
Return type:
List[ProjectSymlink]
```

--------------------------------

### Initialize CryoSPARC Connection

Source: https://tools.cryosparc.com/examples/3dflex-custom-mesh-rigidity-weights.html

Establishes a connection to the CryoSPARC instance. Ensure the host and port are correctly configured for your environment.

```python
import numpy as n

from cryosparc.tools import CryoSPARC

cs = CryoSPARC(host="cryoem5", base_port=40000)
assert cs.test_connection()
```

--------------------------------

### Start Streaming 3D Refinement

Source: https://tools.cryosparc.com/examples/live-session.html

Selects an input volume, updates refinement parameters, and then sets up and enqueues a 3D refinement job. This is typically done after an initial 3D reconstruction.

```python
api.sessions.select_phase2_abinit_volume(project_uid, session_uid, volume_name="volume_class_0")
api.sessions.update_phase2_refine_params(project_uid, session_uid, refine_params)
refine_job_uid = api.sessions.setup_phase2_refine(project_uid, session_uid).uid
api.sessions.enqueue_phase2_refine(project_uid, session_uid)
```

--------------------------------

### get_next_exposure_group_id

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets next exposure group ID.

```APIDOC
## get_next_exposure_group_id(project_uid: str)

### Description
Gets next exposure group ID.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”

### Returns
Successful Response
Return type:
int
```

--------------------------------

### get_generate_intermediate_results_settings

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets generate intermediate result settings.

```APIDOC
## get_generate_intermediate_results_settings(project_uid: str)

### Description
Gets generate intermediate result settings.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”

### Returns
Successful Response
Return type:
GenerateIntermediateResultsSettings
```

--------------------------------

### Initialize CryoSPARC Client

Source: https://tools.cryosparc.com/examples/delete-rejected-exposures.html

Initialize the CryoSPARC client to connect to the CryoSPARC instance. Ensure the host and port are correctly configured for your environment.

```python
from cryosparc.tools import CryoSPARC

cs = CryoSPARC(host="cryoem0.sbi", base_port=40000)
assert cs.test_connection()
```

--------------------------------

### get_generate_intermediate_results_job_types

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets intermediate result job types.

```APIDOC
## get_generate_intermediate_results_job_types()

### Description
Gets intermediate result job types.

### Returns
Successful Response
Return type:
List[str]
```

--------------------------------

### InstanceAuthSessions.load

Source: https://tools.cryosparc.com/api/cryosparc.auth.html

Loads authentication tokens from a specified file path or the default configuration directory.

```APIDOC
## InstanceAuthSessions.load

### Description
Read all auth tokens from the given path. Loads from the user config directory if path is unspecified.

### Method Signature
`load(path: Path | None = None)`
```

--------------------------------

### get_symlinks

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets all symbolic links in the project directory.

```APIDOC
## get_symlinks

### Description
Gets all symbolic links in the project directory.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required

### Response
#### Success Response (200)
- **List[str]** (List[str]) - A list of symbolic link paths.
```

--------------------------------

### Initialize CryoSPARC Connection

Source: https://tools.cryosparc.com/api/cryosparc.tools.html

Instantiate the CryoSPARC class to establish a connection. Provide connection details like URL or host/port and credentials. Defaults can be loaded from environment variables.

```python
from cryosparc.tools import CryoSPARC
cs = CryoSPARC("http://localhost:39000")
```

```python
from cryosparc.tools import CryoSPARC
cs = CryoSPARC(
    email="ali@example.com",
    password="password123",
    host="localhost",
    base_port=39000
)
```

--------------------------------

### ProjectsAPI.get_job_register

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets the job register model for the project.

```APIDOC
## ProjectsAPI.get_job_register

### Description
Gets the job register model for the project.

### Parameters
- **project_uid** (str)

```

--------------------------------

### ProjectsAPI.get_generate_intermediate_results_settings

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets generate intermediate result settings.

```APIDOC
## ProjectsAPI.get_generate_intermediate_results_settings

### Description
Gets generate intermediate result settings.

### Parameters
- ****** (any)

```

--------------------------------

### ls

Source: https://tools.cryosparc.com/api/cryosparc.api.html

List files in the project directory. Can optionally list recursively.

```APIDOC
## ls

### Description
List files in the project directory. Can optionally list recursively.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required
#### Query Parameters
- **recursive** (bool) - Optional
- **path** (str) - Optional

### Response
#### Success Response (200)
- **List[str]** (List[str]) - A list of file paths.
```

--------------------------------

### ProjectsAPI.get_generate_intermediate_results_job_types

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets intermediate result job types.

```APIDOC
## ProjectsAPI.get_generate_intermediate_results_job_types

### Description
Gets intermediate result job types.

```

--------------------------------

### Create an Import Movies Job

Source: https://tools.cryosparc.com/api/cryosparc.controllers.workspace.html

Demonstrates how to create an 'import_movies' job within a workspace and set its parameters. Ensure you have a CryoSPARC instance running and a valid workspace UID.

```python
>>> from cryosparc.tools import CryoSPARC
>>> cs = CryoSPARC("http://localhost:61000")
>>> workspace = cs.find_workspace("P3", "W3")
>>> import_job = workspace.create_job("W1", "import_movies")
>>> import_job.set_param("blob_paths", "/bulk/data/t20s/*.tif")
True
```

--------------------------------

### Initialize CryoSPARC Connection

Source: https://tools.cryosparc.com/examples/connect_series_to_class3D.html

Establishes a connection to the CryoSPARC instance. Ensure the base_port is correctly set for your CryoSPARC installation.

```python
from cryosparc.tools import CryoSPARC

cs = CryoSPARC(base_port=40000)
assert cs.test_connection()
```

--------------------------------

### get_types

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets a list of available job types.

```APIDOC
## get_types

### Description
Gets list of available job types.
```

--------------------------------

### get_directory

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets the job directory for a given job.

```APIDOC
## get_directory

### Description
Gets the job directory for a given job.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required - The unique identifier for the project.
- **job_uid** (str) - Required - The unique identifier for the job.
```

--------------------------------

### Initialize CryoSPARC Client

Source: https://tools.cryosparc.com/examples/hi-res-2d-classes.html

Connect to the CryoSPARC API using the provided host and base port. Ensure the connection is successful.

```python
from cryosparc.tools import CryoSPARC

cs = CryoSPARC(host="cryoem0.sbi", base_port=61000)
assert cs.test_connection()
```

```text
Connection succeeded to CryoSPARC API at http://cryoem0.sbi:61002

```

--------------------------------

### get_targets

Source: https://tools.cryosparc.com/api/cryosparc.tools.html

Get a list of available scheduler targets.

```APIDOC
## get_targets([lane])

### Description
Get a list of available scheduler targets.

### Parameters
- **lane** (str, optional) - The scheduler lane to get targets for.
```

--------------------------------

### Create a 3-Class Ab-initio Job

Source: https://tools.cryosparc.com/api/cryosparc.tools.html

Create a 'homo_abinit' job with specified parameters and input connections. This example shows how to connect the job to existing particle data.

```python
abinit_job = cs.create_job("P3", "W1", "homo_abinit"
    connections={"particles": ("J20", "particles_selected")}
    params={"abinit_K": 3}
)
```

--------------------------------

### get_lanes

Source: https://tools.cryosparc.com/api/cryosparc.tools.html

Get a list of available scheduler lanes.

```APIDOC
## get_lanes()

### Description
Get a list of available scheduler lanes.
```

--------------------------------

### Run cryosparc-tools CLI

Source: https://tools.cryosparc.com/guides/cli.html

This is the general format for running commands with the cryosparc-tools CLI. Use this to access available commands and options.

```bash
python -m cryosparc.tools <command> [options]
```

```bash
python -m cryosparc.tools --help
```

--------------------------------

### find_workspaces

Source: https://tools.cryosparc.com/api/cryosparc.tools.html

Get all workspaces available in the given project.

```APIDOC
## find_workspaces([project_uid, order])

### Description
Get all workspaces available in the given project.

### Parameters
- **project_uid** (str, optional) - The UID of the project.
- **order** (str, optional) - The order in which to retrieve workspaces.
```

--------------------------------

### create

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Creates a new workspace within a specified project.

```APIDOC
## create

### Description
Creates a new workspace.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required - Project UID, e.g., “P3”

#### Request Body
- **title** (str) - Required
- **description** (str) - Optional - Defaults to None
- **created_by_job_uid** (str) - Optional - Defaults to None

### Returns
Successful Response
Return type:
Workspace
```

--------------------------------

### Dataset.descr

Source: https://tools.cryosparc.com/api/cryosparc.dataset.html

Gets a numpy-compatible description for dataset fields.

```APIDOC
## descr

### Description
Get numpy-compatible description for dataset fields.

### Parameters
- **exclude_uid** (bool, optional) – If True, uid field will not be included. Defaults to False.

### Returns
Fields

### Return type
list[Field]
```

--------------------------------

### create

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Creates a new session within a specified project.

```APIDOC
## create

### Description
Creates a new session within a specified project.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”

#### Query Parameters
- **title** (str) - The title of the new session.
- **description** (str) - Optional. A description for the new session. Defaults to None.
- **created_by_job_uid** (str) - Optional. The UID of the job that created this session. Defaults to None.

### Returns
Successful Response

### Return type
Session
```

--------------------------------

### refresh_size

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Starts project size recalculation asynchronously.

```APIDOC
## refresh_size(project_uid: str)

### Description
Starts project size recalculation asynchronously.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”

### Returns
Successful Response
Return type:
None
```

--------------------------------

### Create and Run Template Picker Job

Source: https://tools.cryosparc.com/examples/custom-workflow.html

Initializes and runs a 'template_picker_gpu' job using micrographs and selected templates as input.

```python
template_picker_job = workspace.create_job(
    "template_picker_gpu",
    connections={
        "micrographs": (ctf_estimation_job.uid, "exposures"),
        "templates": (select_blob_templates_job.uid, "templates_selected"),
    },
    params={"diameter": 200},
)
template_picker_job.queue(lane)
template_picker_job.wait_for_done()
```

```text
'completed'
```

--------------------------------

### refresh_size

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Starts project size recalculation asynchronously.

```APIDOC
## refresh_size

### Description
Starts project size recalculation asynchronously.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required

### Response
#### Success Response (200)
- **None** (None) - Successful Response
```

--------------------------------

### Initialize CryoSPARC Connection and Find Project/Workspace

Source: https://tools.cryosparc.com/examples/custom-workflow.html

Initializes a connection to CryoSPARC, tests the connection, and finds a specific project and workspace. Requires host and base port for connection.

```python
from cryosparc.tools import CryoSPARC

cs = CryoSPARC(host="cryoem0.sbi", base_port=61000)
assert cs.test_connection()

project = cs.find_project("P251")
workspace = project.find_workspace("W10")
lane = "cryoem3"

```

--------------------------------

### Create a New Workspace

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Use the `create` method to instantiate a new workspace. Requires a project UID and a title for the workspace.

```python
api.workspaces.create(project_uid="P3", title="My New Workspace")
```

--------------------------------

### get_owner_id

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Get user account ID for the owner of a project.

```APIDOC
## get_owner_id(project_uid: str)

### Description
Get user account ID for the owner of a project.

### Parameters
#### Path Parameters
- **project_uid** (str) - Project UID, e.g., “P3”

### Returns
Successful Response
Return type:
str
```

--------------------------------

### Download and Upload Dataset from Remote Project

Source: https://tools.cryosparc.com/_sources/intro.md

This example shows how to download a dataset from a remote project, perform modifications (indicated by '...'), and then upload the modified dataset back.

```py
particles = project.download_dataset("J43/particles.cs")
shift_y, shift_x = particles["alignments2D/shift"].T
...
project.upload_dataset("J43/particles.cs", particles)
```

--------------------------------

### get_owner_id

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Get user account ID for the owner of a project.

```APIDOC
## get_owner_id

### Description
Get user account ID for the owner of a project.

### Parameters
#### Path Parameters
- **project_uid** (str) - Required

### Response
#### Success Response (200)
- **str** (str) - The user ID of the project owner.
```

--------------------------------

### run()

Source: https://tools.cryosparc.com/api/cryosparc.cli.html

Runs the command-line interface.

```APIDOC
## run([name])

### Description
Run command line interface.

### Parameters
* **name** (str) - Optional. Defaults to 'cryosparc.tools'. Description not available in source.
```

--------------------------------

### get_active_licenses_count

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Gets the number of acquired licenses for running jobs.

```APIDOC
## get_active_licenses_count

### Description
Gets number of acquired licenses for running jobs.
```

--------------------------------

### External API: Get Changelog

Source: https://tools.cryosparc.com/api/cryosparc.api.html

Retrieves the changelog for CryoSPARC.

```APIDOC
## Get Changelog

### Description
Retrieves the changelog for CryoSPARC.

### Returns
Successful Response

### Return Type
Dict[str, Any]
```