CryoSPARC Live Connection

Smartscope/core/pipelines/__init__.py

@@ -5,4 +5,4 @@
 from .smartscope_preprocessing_cmd_kwargs import SmartScopePreprocessingCmdKwargs
 from .smartscope_preprocessing_pipeline import SmartscopePreprocessingPipeline
 from .smartscope_preprocessing_pipeline_form import SmartScopePreprocessingPipelineForm
-from .cryosparc_live import CryoSPARC
+from .cryosparc_live import CryoSPARCPipeline

Smartscope/core/pipelines/cryosparc_live.py

@@ -19,30 +19,51 @@
 from .smartscope_preprocessing_pipeline_form import SmartScopePreprocessingPipelineForm
 from .smartscope_preprocessing_cmd_kwargs import SmartScopePreprocessingCmdKwargs
 
+from typing import Union
+from pathlib import Path
+from pydantic import BaseModel, Field, validator
+
 logger = logging.getLogger(__name__)
 
 from django import forms
+from cryosparc.tools import CryoSPARC
 
 class CryoSPARCPipelineForm(forms.Form):
-    cs_address = forms.URLField(label='CryoSPARC URL:',help_text='Web address of CryoSPARC installation (must be accessible from the SmartScope computer).')
+    cs_address = forms.CharField(label='CryoSPARC URL:',help_text='Web address of CryoSPARC installation (must be accessible from the SmartScope computer).')
     cs_port = forms.IntegerField(label='CryoSPARC Port:',help_text='Port of CryoSPARC installation. Defaults to 39000 if not set')
     cs_license = forms.CharField(label='CryoSPARC License Key',help_text='CryoSPARC License Key')
-    cs_project = forms.IntegerField(label='CryoSPARC Project # P',
-        help_text='Enter the project number of the CryoSPARC project you would like to spawn the Live sessions in. Omit the P at the beginning'
-        ) 
+    cs_email = forms.CharField(label='CryoSPARC User Email',help_text='CryoSPARC User Email Address')
+    cs_password = forms.CharField(label='CryoSPARC User Password',help_text='CryoSPARC User Password')
+    cs_project = forms.IntegerField(label='CryoSPARC Project # P',help_text='Enter the project number of the CryoSPARC project you would like to spawn the Live sessions in. Omit the P at the beginning')
     cs_worker_processes=forms.IntegerField(label='# of pre-processing workers:',help_text='Number of worker processes to spawn')
     cs_preprocessing_lane = forms.CharField(label='Name of pre-processing lane:',help_text='Name of lane to use for CryoSPARC Live preprocessing lane')
-    frames_directory = forms.CharField(help_text='Locations to look for the frames file other. '+ \
-        'Will look in the default smartscope/movies location by default.')
+    frames_directory = forms.CharField(help_text='Absolute path for frame directory relative to CryoSPARC Master instance')
+    cs_dose=forms.FloatField(label='Dose',help_text='Total dose in e/A2')
+    cs_apix=forms.FloatField(label='Pixel Size',help_text='Angstroms per pixel')
+    cs_lanes=forms.CharField(label='Worker Lane',help_text='Name of CryoSPARC Live Worker Lane')
 
     def __init__(self, *args,**kwargs):
         super().__init__(*args, **kwargs)
         for visible in self.visible_fields():
             visible.field.widget.attrs['class'] = 'form-control'
             visible.field.required = False
 
-
-class CryoSPARC(PreprocessingPipeline):
+class CryoSPARCCmdKwargs(BaseModel):
+    cs_address:str = ""
+    cs_port:int = 39000
+    cs_license:str = ""
+    cs_email:str = ""
+    cs_password:str = ""
+    cs_project:int = 9999
+    cs_worker_processes:int = 1
+    cs_preprocessing_lane:str = ""
+    frames_directory:str = ""
+    cs_dose:float = 50.0
+    cs_apix:float = 1.0
+    cs_lanes:str = ""
+
+
+class CryoSPARCPipeline(PreprocessingPipeline):
     verbose_name = 'CryoSPARC Live Pre-Processing Pipeline'
     name = 'cryoSPARC'
     description = 'Spawn CryoSPARC Live sessions at each grid. Requires a functional CryoSPARC installation.'
@@ -51,7 +72,7 @@ class CryoSPARC(PreprocessingPipeline):
     child_process = []
     to_update = []
     incomplete_processes = []
-    cmdkwargs_handler = SmartScopePreprocessingCmdKwargs
+    cmdkwargs_handler = CryoSPARCCmdKwargs
     pipeline_form= CryoSPARCPipelineForm
 
     def __init__(self, grid: AutoloaderGrid, cmd_data:Dict):
@@ -60,16 +81,66 @@ def __init__(self, grid: AutoloaderGrid, cmd_data:Dict):
         self.detector = self.grid.session_id.detector_id
         self.cmd_data = self.cmdkwargs_handler.parse_obj(cmd_data)
         logger.debug(self.cmd_data)
-        self.frames_directory = [Path(self.detector.frames_directory)]
-        if self.cmd_data.frames_directory is not None:
-            self.frames_directory.append(self.cmd_data.frames_directory)
+
+        self.license = self.cmd_data.cs_license
+        self.host = self.cmd_data.cs_address
+        self.base_port = self.cmd_data.cs_port
+        self.email = self.cmd_data.cs_email
+        self.password = self.cmd_data.cs_password
+        self.project = 'P' + str(self.cmd_data.cs_project)
+        self.frames_directory = self.cmd_data.frames_directory
+        self.dose = self.cmd_data.cs_dose
+        self.apix = self.cmd_data.cs_apix
+        self.lane = self.cmd_data.cs_lanes
+
+        self.cs_session = ""
 
     def start(self): #Abstract Class Function - Required
-        pass
+
+        #Setup connection to CryoSPARC Instance
+        cs_instance = CryoSPARC(license=self.license,host=self.host,base_port=self.base_port,email=self.email,password=self.password)
+        csparc_debug = str(cs_instance.test_connection())
+        logger.debug(f'CryoSPARC Connection Test: {csparc_debug}')
+
+        #Need to check here if session already exists. If so, skip creation, if not, create.
+
+        #Create new CryoSPARC Live session
+        cs_session = cs_instance.rtp.create_new_live_workspace(project_uid=str(self.project), created_by_user_id=str(cs_instance.cli.get_id_by_email(self.email)), title=str(self.grid.session_id))
+        return cs_session
+
+        #Setup lanes
+        cs_instance.rtp.update_compute_configuration(project_uid=str(self.project), session_uid=cs_session, key='phase_one_lane', value=str(self.lane))
+        cs_instance.rtp.update_compute_configuration(project_uid=str(self.project), session_uid=cs_session, key='phase_one_gpus', value=2)
+        cs_instance.rtp.update_compute_configuration(project_uid=str(self.project), session_uid=cs_session, key='phase_two_lane', value=str(self.lane))
+        cs_instance.rtp.update_compute_configuration(project_uid=str(self.project), session_uid=cs_session, key='auxiliary_lane', value=str(self.lane))
+
+        #Setup exposure group
+        cs_instance.rtp.exposure_group_update_value(project_uid=str(self.project), session_uid=cs_session, exp_group_id=1, name='file_engine_watch_path_abs', value=str(self.frames_directory))
+        cs_instance.rtp.exposure_group_update_value(project_uid=str(self.project), session_uid=cs_session, exp_group_id=1, name='file_engine_filter', value='.tif')
+        cs_instance.rtp.exposure_group_finalize_and_enable(project_uid=str(self.project), session_uid=cs_session, exp_group_id=1)
+
+        #Motion Correction Settings
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='mscope_params', param_name='accel_kv', value=float(self.microscope.voltage))
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='mscope_params', param_name='cs_mm', value=float(self.microscope.spherical_abberation))
+
+        ##Need to check for if files have been written here, and get values from .mdoc file.
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='mscope_params', param_name='total_dose_e_per_A2', value=float(self.dose))
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='mscope_params', param_name='psize_A', value=float(self.apix))
+        ##Also need gain controls here (Flip/rotate)
+
+        #Extraction Settings
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='blob_pick', param_name='diameter', value=100)
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='blob_pick', param_name='diameter_max', value=200)
+        cs_instance.rtp.set_param(project_uid=str(self.project), session_uid=cs_session, param_sec='extraction', param_name='box_size_pix', value=440)
+
+        #Start the session
+        cs_instance.rtp.start_session(project_uid=str(self.project), session_uid=cs_session, user_id=cs_instance.cli.get_id_by_email(self.email))
 
     def stop(self):  #Abstract Class Function - Required
-        pass
+        #Turn off live session
+        cs_instance = CryoSPARC(license=self.license,host=self.host,base_port=self.base_port,email=self.email,password=self.password)
+        cs_instance.rtp.pause_session(project_uid=str(self.project), session_uid=self.cs_session)
 
     def check_for_update(self, instance):  #Abstract Class Function - Required
+        #Here should probably go some logic that will get the hole and image, check CryoSPARC for existing thumbnail and data, and update the object
         pass
-

Smartscope/core/preprocessing_pipelines.py

@@ -9,10 +9,10 @@
 
 logger = logging.getLogger(__name__)
 
-from .pipelines import PreprocessingPipelineCmd, SmartscopePreprocessingPipeline, CryoSPARC
+from .pipelines import PreprocessingPipelineCmd, SmartscopePreprocessingPipeline, CryoSPARCPipeline
 
 
-PREPROCESSING_PIPELINE_FACTORY = dict(smartscopePipeline=SmartscopePreprocessingPipeline, cryoSPARC=CryoSPARC)
+PREPROCESSING_PIPELINE_FACTORY = dict(smartscopePipeline=SmartscopePreprocessingPipeline, cryoSPARC=CryoSPARCPipeline)
 
 def load_preprocessing_pipeline(file:Path):
     if file.exists():