Merge pull request #78 from instamatic-dev/tweaks

Maintenance and documentation

Author: stefsmeets

.bumpversion.cfg

@@ -1,16 +1,16 @@
 [bumpversion]
-current_version = 1.10.0
+current_version = 2.0.0
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved
 
-[bumpversion:file:instamatic/__init__.py]
+[bumpversion:file:src/instamatic/__init__.py]
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'
 
-[bumpversion:file:setup.cfg]
-search = version = {current_version}
-replace = version = {new_version}
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:file:CITATION.cff]
 search = version: "{current_version}"

.github/workflows/publish.yml

@@ -12,16 +12,16 @@ jobs:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
       with:
-        python-version: 3.9
+        python-version: '3.11'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-        python setup.py sdist bdist_wheel
+        pip install -U build setuptools wheel
+        python -m build --no-isolation
 
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yml

@@ -37,7 +37,7 @@ jobs:
       id: cache-python-env
       with:
         path: ${{ env.pythonLocation }}
-        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.cfg') }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
 
     - name: Install
       if: steps.cache-python-env.outputs.cache-hit != 'true'

CITATION.cff

@@ -27,5 +27,5 @@ doi: "10.5281/zenodo.1090388"
 license: "BSD-3-Clause"
 message: "If you use this software, please cite it using these metadata."
 title: Instamatic
-version: "1.10.0"
+version: "2.0.0"
 ...

MANIFEST.in

@@ -13,17 +13,17 @@ include setup_win.bat
 include tests/*.py
 include tests/config/*.yaml
 include tests/config/*/*.yaml
-include instamatic/camera/*.dll
-include instamatic/camera/*.h
-include instamatic/camera/*.lockfile
-include instamatic/camera/*.md
-include instamatic/camera/tpx/*.bpc
-include instamatic/camera/tpx/*.dacs
-include instamatic/camera/tpx/*.txt
-include instamatic/config/*.yaml
-include instamatic/config/alignments/*.yaml
-include instamatic/config/calibration/*.yaml
-include instamatic/config/camera/*.yaml
-include instamatic/config/microscope/*.yaml
-include instamatic/config/scripts/*.md
-include instamatic/neural_network/*.p
+include src/instamatic/camera/*.dll
+include src/instamatic/camera/*.h
+include src/instamatic/camera/*.lockfile
+include src/instamatic/camera/*.md
+include src/instamatic/camera/tpx/*.bpc
+include src/instamatic/camera/tpx/*.dacs
+include src/instamatic/camera/tpx/*.txt
+include src/instamatic/config/*.yaml
+include src/instamatic/config/alignments/*.yaml
+include src/instamatic/config/calibration/*.yaml
+include src/instamatic/config/camera/*.yaml
+include src/instamatic/config/microscope/*.yaml
+include src/instamatic/config/scripts/*.md
+include src/instamatic/neural_network/*.p

docs/config.md

@@ -26,7 +26,7 @@ instamatic.autoconfig.exe
 ```
 To help generate some of the input files (in particular templates for the microscope/calibration files).
 
-Examples of configuration files can be found [here](https://github.com/instamatic-dev/instamatic/tree/main/instamatic/config).
+Examples of configuration files can be found [here](https://github.com/instamatic-dev/instamatic/tree/main/src/instamatic/config).
 
 ## settings.yaml
 

docs/examples/montage_processing.ipynb

@@ -319,7 +319,7 @@
     "    for i, image in enumerate(buffer):\n",
     "        x, y, z, _, _ = stagepos[i]\n",
     "        shape = image.shape\n",
-    "        # binsize = ctrl.cam.getBinning()\n",
+    "        # binsize = ctrl.cam.get_binning()\n",
     "\n",
     "        d = {}\n",
     "        d['StageXYZ'] = x / 1000, y / 1000, z / 1000\n",

docs/merlin.md

@@ -4,7 +4,7 @@ The [MerlinEM detector](https://quantumdetectors.com/products/merlinem/) by Quan
 
 Instamatic communicates with the Merlin control software via TCP/IP connection. This means that there is a fast connection with little overhead when collecting data.
 
-In continous read/write mode, instamatic can achieve gapless data acquisition `MerlinCamera.getMovie()`. When continuously collecting single images using `MerlinCamera.getImage()`, there is a ~3 ms overhead per frame.
+In continous read/write mode, instamatic can achieve gapless data acquisition `MerlinCamera.get_movie()`. When continuously collecting single images using `MerlinCamera.get_image()`, there is a ~3 ms overhead per frame.
 
 ## Setup
 
@@ -16,7 +16,7 @@ camera: merlin
 
 You can set up the parameters for the Merlin camera through `camera/merlin.yaml` in your config directory.
 
-For an example config file, see: [`camera/merlin.yaml`](https://github.com/instamatic-dev/instamatic/blob/main/instamatic/config/camera/merlin.yaml). [Click here](/config.md#camerayaml) to go to the page with all common camera configuration parameters.
+For an example config file, see: [`camera/merlin.yaml`](https://github.com/instamatic-dev/instamatic/blob/main/src/instamatic/config/camera/merlin.yaml). [Click here](/config.md#camerayaml) to go to the page with all common camera configuration parameters.
 
 In addition, the Merlin camera has the following parameters to configure:
 
@@ -34,18 +34,24 @@ host: '10.0.0.123'
 
 **detector_config**
 : The parameters under `detector_config` are directly sent to the Merlin software when instamatic starts.
-These can be used to put the Merlin in the desired state for data acquisition. Check the Merlin documention for more information.
+These can be used to put the Merlin in the desired state for data acquisition. Any command with a `SET` type can be adjusted. Check the Merlin EM documention for more information.
+
+: The default sets continuous read-write mode and 12-bit mode to minimize the gap between frames. It also disables automatic file writing (`FILEENABLE`) and image processing by Merlin, and enables headless `RUNHEADLESS` mode for faster throughput. If you don't want this, you can delete these lines or modify them.
 
-: For example:
+```yaml
+detector_config:
+  CONTINUOUSRW: 1
+  COUNTERDEPTH: 12
+  FILEENABLE: 0
+  RUNHEADLESS: 1
+```
+
+: You could for example also set the thresholds and bias in the instamatic config by adding these lines:
 ```yaml
 detector_config:
   THRESHOLD0: 120
   THRESHOLD1: 40
   HVBIAS: 511
-  COUNTERDEPTH: 12
-  FILEENABLE: 0
-  CONTINUOUSRW: 1
-  RUNHEADLESS: 0
 ```
 
 ## Notes on using instamatic with Merlin

docs/programs.md

@@ -604,7 +604,7 @@ instamatic.xdsserver [-h]
 
 ## instamatic.temserver_fei
 
-Utility script to enable rotation control from a dmscript. See [https://github.com/instamatic-dev/instamatic/tree/master/dmscript] for usage.
+Utility script to enable rotation control from a dmscript. See [https://github.com/instamatic-dev/InsteaDMatic] for usage.
 
 **Usage:**  
 ```bash

docs/tem_api.md

@@ -31,7 +31,7 @@ ctrl = TEMController.initialize(tem_name='jeol', cam_name=None)
 
 Once a `ctrl` (control) object has been initialized, it becomes possible to play around with the lenses and stage interactively. Type `ctrl.` and hit `tab` to see the autocomplete options. Or write use `?` to request the doc string for a function (e.g. `TEMController.initialize?`).
 
-Based on this you can write your own python scripts to control the microscope and/or camera. See in `instamatic/instamatic/experiments/cred/experiment.py` for an idea how this is used. All the microscope control interface can be found in `instamatic/TEMController/`
+Based on this you can write your own python scripts to control the microscope and/or camera. See in `src/instamatic/experiments/cred/experiment.py` for an idea how this is used. All the microscope control interface can be found in `src/instamatic/TEMController/`
 
 The `ctrl` object allows full control over the electron microscope. For example, to read out the position of the sample stage:
 ```python