Skip to content

New selectors #255

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
JoQCcoz merged 2 commits into from
Mar 13, 2024
Merged

New selectors #255

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
bc69de7
remove tilt angle from card temporarily
JoQCcoz Mar 13, 2024
c5c9055
removing pydantic deprecated functions
JoQCcoz Mar 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions Smartscope/core/config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ def register_plugins(directories, factory):
module = importlib.import_module('.'.join(split[:-1]))
out_class = getattr(module, split[-1])

factory[data['name']] = out_class.parse_obj(data)
factory[data['name']] = out_class.model_validate(data)

def get_active_plugins_list(external_plugins_directory,external_plugins_list):
with open(external_plugins_list,'r') as file:
Expand All @@ -43,7 +43,7 @@ def register_protocols(directories:List[Path], factory):
logger.debug(f'Registering protocol {file}')
with open(file) as f:
data = yaml.safe_load(f)
factory[data['name']] = BaseProtocol.parse_obj(data)
factory[data['name']] = BaseProtocol.model_validate(data)

def register_external_plugins(external_plugins_list,plugins_factory,protocols_factory):
for path in external_plugins_list:
Expand Down
2 changes: 1 addition & 1 deletion Smartscope/core/mesh_rotation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ def calculate_hole_geometry(grid:AutoloaderGrid):
pixel_size = targets[0].parent.pixel_size
logger.debug(f'Calculating hole geometry for grid {grid} with {len(targets)} holes and mesh spacing: {mesh_spacing} um. Pixel size of {targets[0].parent}: {pixel_size} A.')
rotation, spacing = get_mesh_rotation_spacing(coords, mesh_spacing / pixel_size * 10_000)

geometry = GridGeometry.load(directory=grid.directory)
geometry.set_geometry(level=GridGeometryLevel.SQUARE, spacing=spacing, rotation=rotation)
geometry.save(directory=grid.directory)
Expand Down
2 changes: 1 addition & 1 deletion Smartscope/server/api/templates/holecard.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ <h5 class="col-19 card-title m-0">Hole {{hole.hole_id.number}}-{{hole.number}}</
<p class="card-text text-left m-0">Astig: {{hole.astig|floatformat:0}} &#8491;</p>
<p class="card-text text-left m-0">Astig Angle: {{hole.angast|floatformat:0}} &#176;</p>
<p class="card-text text-left m-0">Ice thickness: {{hole.ice_thickness}} nm</p>
<p class="card-text text-left m-0">Tilt angle: {{hole.tilt_angle|floatformat:1}} &#176;</p>
<!-- <p class="card-text text-left m-0">Tilt angle: {{hole.tilt_angle|floatformat:1}} &#176;</p> -->
<p class="card-text text-left m-0">Targeting offset: {{hole.offset|floatformat:1}} &mu;m;</p>
</div>
<div class="card-footer py-1">
Expand Down