Merge pull request #245 from NIEHS/stable

merge stable into latest

Smartscope/core/autoscreen.py

@@ -45,12 +45,13 @@ def autoscreen(session_id:str):
         logger.info(f'Process: {process}')
         logger.info(f'Session: {session}')
         logger.info(f"Grids: {', '.join([grid.__str__() for grid in grids])}")
-        scopeInterface = select_microscope_interface(microscope)
+        scopeInterface, additional_settings = select_microscope_interface(microscope)
 
         with scopeInterface(
                 microscope = Microscope.model_validate(session.microscope_id),
                 detector= Detector.model_validate(session.detector_id) ,
-                atlas_settings= AtlasSettings.model_validate(session.detector_id)
+                atlas_settings= AtlasSettings.model_validate(session.detector_id),
+                additional_settings=additional_settings
             ) as scope:
 
             logger.debug(f'Main Log handlers:{logger.handlers}')

Smartscope/core/db_manipulations.py

@@ -134,7 +134,7 @@ def viewer_only(user):
 
 def group_holes_for_BIS(hole_models, max_radius=4, min_group_size=1, queue_all=False, iterations=500, score_weight=2):
     if len(hole_models) == 0:
-        return
+        return  hole_models
     logger.debug(
         f'grouping params, max radius = {max_radius}, min group size = {min_group_size}, queue all = {queue_all}, max iterations = {iterations}, score_weight = {score_weight}')
     # Extract coordinated for the holes

Smartscope/core/grid/finders.py

@@ -14,6 +14,7 @@ def find_targets(montage: Montage, methods: list):
             targets, success, additional_outputs  = method.run(montage=montage)
         except Exception as err:
             logger.exception(err)
+            success = False
             continue
         if success:
             logger.debug(f"{method} was successful: {success}, '+ \
@@ -22,4 +23,4 @@ def find_targets(montage: Montage, methods: list):
                 return targets, method.name, method.name, additional_outputs
             else:
                 return targets, method.name, None, additional_outputs
-        return [], '', None, dict()
+    return [], '', None, dict()

Smartscope/core/interfaces/jeolserialem_interface.py

@@ -1,5 +1,6 @@
 import serialem as sem
 from typing import Callable
+from pydantic import BaseModel
 import time
 import logging
 from .serialem_interface import SerialemInterface
@@ -14,9 +15,12 @@ def wrapper(*args, **kwargs):
         sem.ReInsertAperture(0)
     return wrapper
 
+class JEOLadditionalSettings(BaseModel):
+    transfer_cartridge_path: str = 'C:\Program Data\SerialEM\PyTool\Transfer_Cartridge.bat'
 
 class JEOLSerialemInterface(SerialemInterface):
-
+    additional_settings: JEOLadditionalSettings = JEOLadditionalSettings()
+
     def checkPump(self, wait=30):
         pass
 
@@ -31,16 +35,16 @@ def atlas(self, *args, **kwargs):
         if not self.microscope.apertureControl:
             return super().atlas(*args,**kwargs)
         remove_condenser_aperture(
-            super().atlas(*args,**kwargs)
-        )
+            super().atlas)(*args,**kwargs)
+
 
     def loadGrid(self, position):
         if self.microscope.loaderSize > 1:
             sem.Delay(5)
             sem.SetColumnOrGunValve(0)
             sem.Delay(5)
             ## HARCODED FOR NOW SINCE THE EXECUTABLE SHOULD BE THERE IN ALL SCOPES
-            sem.RunInShell(f'C:\Program Data\SerialEM\PyTool\Transfer_Cartridge.bat {position}')
+            sem.RunInShell(f"""{self.additional_settings.transfer_cartridge_path} "{position} 3 0" """)
             sem.Delay(5)
         sem.SetColumnOrGunValve(1)
 

Smartscope/core/interfaces/microscope_interface.py

@@ -14,11 +14,13 @@ class MicroscopeInterface(ABC):
     detector: Detector
     atlas_settings:AtlasSettings
     state: MicroscopeState = MicroscopeState()
+    additional_settings: dict = None 
     has_hole_ref: bool = False
     hole_crop_size: int = 0
     focus_position_set: bool = False
 
     def __enter__(self):
+        logger.debug(f'Additional settings set: {self.additional_settings}')
         self.connect()
         return self
 

Smartscope/core/interfaces/microscope_methods.py

@@ -1,14 +1,30 @@
+import yaml
+import logging
+from Smartscope.core.settings.worker import SMARTSCOPE_CUSTOM_CONFIG
 from .fakescope_interface import FakeScopeInterface
 from .tfsserialem_interface import TFSSerialemInterface
-from .jeolserialem_interface import JEOLSerialemInterface
+from .jeolserialem_interface import JEOLSerialemInterface, JEOLadditionalSettings
+
+logger = logging.getLogger(__name__)
 
 def select_microscope_interface(microscope):
+    additional_settings_file = SMARTSCOPE_CUSTOM_CONFIG / f'{microscope.microscope_id}.yaml'
+    additional_settings = dict()
+    logger.debug(f'Additional settings file: {additional_settings_file}')
+    if additional_settings_file.exists():
+        with open(additional_settings_file, 'r') as yaml_file:
+            logger.info(f'Loading additional settings from {additional_settings_file}')
+            additional_settings = yaml.safe_load(yaml_file)
+
     if microscope.serialem_IP == 'xxx.xxx.xxx.xxx':
-        # logger.info('Setting scope into test mode')
-        return FakeScopeInterface
+        logger.info('Setting scope into test mode')
+        return FakeScopeInterface, additional_settings
 
     if microscope.vendor == 'JEOL':
-        # logger.info('Using the JEOL interface')
-        return JEOLSerialemInterface
+        logger.info('Using the JEOL interface')
+
+        return JEOLSerialemInterface, JEOLadditionalSettings.model_validate(additional_settings)
+
+    logger.info('Using the TFS interface')
 
-    return TFSSerialemInterface
+    return TFSSerialemInterface, additional_settings

Smartscope/core/interfaces/tfsserialem_interface.py

@@ -42,6 +42,15 @@ def wrapper(*args, **kwargs):
         logger.info(msg)
         sem.ReInsertAperture(Aperture.OBJECTIVE)
         time.sleep(wait)
+
+    def no_wrap(*args,**kwargs):
+        msg = 'Objective aperture already out. Skipping removal and reinstertion.'
+        sem.Echo(msg)
+        logger.info(msg)
+        function(*args, **kwargs)
+
+    if sem.ReportApertureSize(Aperture.OBJECTIVE) == 0:
+        return no_wrap
     return wrapper
 
 class TFSSerialemInterface(SerialemInterface):

Smartscope/core/main_commands.py

@@ -4,6 +4,7 @@
 import json
 from django.db import transaction
 from django.conf import settings
+from django.core.cache import cache
 
 from Smartscope.core.models import *
 from Smartscope.core.test_commands import *
@@ -52,7 +53,7 @@ def add_holes(id, targets):
     instance = SquareModel.objects.get(pk=id)
     montage = Montage(name=instance.name, working_dir=instance.grid_id.directory)
     montage.load_or_process()
-    targets = np.array(targets) + np.array([0, instance.shape_x])
+    targets = np.array(targets) 
     hole_size = holeSize if (holeSize := instance.grid_id.holeType.hole_size) is not None else 1.2
     targets = list(map(lambda t: convert_centers_to_boxes(
         t, montage.pixel_size, montage.shape_x, montage.shape_y, hole_size), targets))
@@ -76,18 +77,21 @@ def add_holes(id, targets):
     return holes
 
 
-def add_single_targets(id, *args):
-    logger.info(f'Adding {len(args)} targets to square {id}')
+def add_single_targets(id_, *args):
+    logger.info(f'Adding {len(args)} targets to square {id_}')
     targets = []
     for i in args:
         j = i.split(',')
         j = [float(k) for k in j]
 
         targets.append(j)
     logger.debug(targets)
-    holes = add_holes(id=id, targets=targets)
+    holes = add_holes(id=id_, targets=targets)
+
+    logger.debug(f'Successfully added {len(holes)} targets.')
+    cache_key = f'{id_}_targets_methods'
+    cache.delete(cache_key)
 
-    logger.debug(holes)
 
 
 def check_pause(microscope_id: str, session_id: str):
@@ -241,4 +245,24 @@ def get_atlas_to_search_offset(detector_name,maximum=0):
         return
     print('Skip setting values')
 
+
+def export_grid(grid_id, export_to=''):
+    from Smartscope.core.utils.export_import import export_grid
+    if export_to == '':
+        export_to = os.path.join(grid.directory, 'export.yaml')
+        print(f'Export path not specified. Exporting to default loacation: {export_to}')
+    grid = AutoloaderGrid.objects.get(grid_id=grid_id)
+    export_grid(grid, export_to=export_to)
+    print('Done.')
+
+def import_grid(file:str):
+    from Smartscope.core.utils.export_import import import_grid
+    if not Path(file).exists():
+        print(f'File {file} does not exist.')
+        return
+    print(f'Importing {file} into the smartscope database.')
+    import_grid(file)
+    print('Done.')
+
+
 

Smartscope/core/models/screening_session.py

@@ -29,7 +29,7 @@ def root_directories(session):
             root_directories.append(custom_group_path.path)
 
     if settings.USE_STORAGE:
-        root_directories.append(settings.AUTOSCREENDIR)
+        # root_directories.append(settings.AUTOSCREENDIR)
         if (groupname:=session.group.name) is not None:
             root_directories.append(os.path.join(settings.AUTOSCREENDIR,groupname))
         else: 

Smartscope/core/svg_plots.py

@@ -88,6 +88,7 @@ def drawAtlas(atlas, targets, display_type, method) -> draw.Drawing:
     labels_list = []
     for i in targets:
         color, label, prefix = css_color(i, display_type, method)
+
         if color is not None:
             sz = floor(sqrt(i.area))
             finder = list(i.finders.all())[0]
@@ -132,6 +133,7 @@ def drawSquare(square, targets, display_type, method) -> draw.Drawing:
     for i in targets:
 
         color, label, prefix = css_color(i, display_type, method)
+        # logger.debug(f'{i.number} -> {color}')
         if color is not None:
             finder = list(i.finders.all())[0]
             if not finder.is_position_within_stage_limits():

Smartscope/core/test_commands.py

@@ -99,7 +99,7 @@ def refine_pixel_size_from_targets(instances, spacings) -> Tuple[float, float]:
 
 
 def test_finder(plugin_name: str, raw_image_path: str, output_dir: str, repeats=1):  # output_dir='/mnt/data/testing/'
-    from build_smartscope.SmartScope.Smartscope.lib.image.montage import Montage
+    from Smartscope.lib.image.montage import Montage
     from Smartscope.lib.image_manipulations import auto_contrast, save_image
     import cv2
     import math

Smartscope/lib/Finders/AIFinder/detectors/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2022, Bartesaghi Lab (Duke University)
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.