Merge pull request #128 from DeMarcoLab/v0.2-dev

v0.2.4 Release

.gitignore

@@ -25,3 +25,4 @@ old_protocol/*.y*ml
 old_protocol/*
 dist/*
 autolamella/db/fibsem.db
+autolamella/liftout/log/*

README.md

@@ -10,64 +10,24 @@ AutoLamella is a python package for automated cryo-lamella preparation with focu
 
 ## Install
 
-### Install OpenFIBSEM
-Clone this repository: 
+### Recommended Installation Guide
 
+Create a new virtual environment from the Anaconda Prompt terminal:
 ```
-$ git clone https://github.com/DeMarcoLab/fibsem.git
-```
-
-Install dependencies and package
-```bash
-$ cd fibsem
-$ conda env create -f environment.yml
+$ conda create -n fibsem python=3.9 pip
 $ conda activate fibsem
-$ pip install -e .
-
+$ pip install autolamella 
 ```
-### Install autolamella package
-Clone this repository: 
+### Running Autolammela
 
-```
-$ git clone https://github.com/DeMarcoLab/autolamella.git
-```
-
-Install dependencies and package
-```bash
-$ conda activate fibsem
-$ cd autolamella
-$ pip install -e .
-$ pip install pywin32==228
-$ conda install -c conda-forge petname
+Open the Anaconda Prompt terminal and run the following commands.
 
 ```
+$ conda activate fibsem
+$ autolamella_ui
 
-### Install AutoScript
-You will also need to install AutoScript 4.6+. 
-
-Please see the [Installation Guide](INSTALLATION.md) for detailed instructions.
-
-Copy AutoScript /into home/user/miniconda3/envs/fibsem/lib/python3.9/site-packages/
-
-### Install TESCAN Automation SDK
-
-Ideally, please install and set up the conda environment first before proceeding to install this SDK
-
-Run the Tescan-Automation-SDK-Installer-3.x.x.exe file
-
-When asked for the python interpretor, select the existing conda environment for FIBSEM, if this python interpretor is not available, see detailed installation guide for a work around
-
-See [Installation Guide](INSTALLATION.md) for full details
-
-
-### Getting started 
-To run autolamella:
-```bash
-$ conda activate autolamella
-$ autolamella
 ```
-![UI](docs/img/ui.png)
-
+![ui_new](docs/img/ui_new.png)
 
 ## Citation
 If you find this useful, please cite our work.

autolamella/config.py

@@ -1,17 +1,19 @@
 import os
 from pathlib import Path
-
+import autolamella
 
 BASE_PATH: Path = os.path.dirname(__file__)
 LOG_PATH: Path = os.path.join(BASE_PATH, 'log')
 CONFIG_PATH: Path = os.path.join(BASE_PATH)
 PROTOCOL_PATH: Path = os.path.join(BASE_PATH, "protocol", "protocol.yaml")
 SYSTEM_PATH: Path = os.path.join(CONFIG_PATH, "system.yaml")
-
+DESKTOP_SHORTCUT_PATH= os.path.dirname(autolamella.__path__[0]) 
 
 EXPERIMENT_NAME = "AutoLamella"
 HFW_THRESHOLD = 0.005 # 0.5% of the image height
 
+__AUTOLAMELLA_METHODS__ = ["Autolamella-Default", "Autolamella-Waffle"]#, "Autoliftout-Default", "Autoliftout-Serial-Liftout"]
+
 DEFAULT_PROTOCOL = {
 
 "main_headers" : {
@@ -29,10 +31,9 @@
 },
 
 "lamella_headers" : {
-    "beam_shift_attempts": 3,
+    "alignment_attempts": 3,
     "lamella_width": 10.e-6,
     "lamella_length": 10.e-6,
-    "alignment_current": "Imaging Current",
 },
 
 "protocol_stage_1" : {
@@ -71,4 +72,6 @@
 
 
 ####### FEATURE FLAGS
-_MINIMAP_VISUALISATION = True
+_MINIMAP_VISUALISATION = True
+_AUTO_SYNC_MINIMAP = True
+_REGISTER_METADATA = True

autolamella/liftout/__init__.py

@@ -0,0 +1,5 @@
+try:
+    import importlib.metadata
+    __version__ = importlib.metadata.version('liftout')
+except ModuleNotFoundError:
+    __version__ = "unknown"