Update documentation

.pre-commit-config.yaml

@@ -20,6 +20,11 @@ repos:
     rev: v0.2.0
     hooks:
       - id: nbcheckorder
+        # This notebook is not executed at all, which fails the check
+        exclude: |
+          (?x)^(
+            docs/examples/montage_processing.ipynb
+          )$
   - repo: https://github.com/myint/docformatter
     rev: master  # https://github.com/PyCQA/docformatter/issues/293
     hooks:

docs/api/components_deflectors.md

@@ -0,0 +1 @@
+::: instamatic.microscope.components.deflectors

docs/api/components_lenses.md

@@ -0,0 +1 @@
+::: instamatic.microscope.components.lenses

docs/api/components_stage.md

@@ -0,0 +1 @@
+::: instamatic.microscope.components.stage

docs/api/components_states.md

@@ -0,0 +1 @@
+::: instamatic.microscope.components.states

docs/api/controller.md

@@ -0,0 +1 @@
+::: instamatic.controller

docs/examples/grid_montage_collection.ipynb

@@ -47,10 +47,12 @@
     }
    ],
    "source": [
-    "from instamatic import TEMController\n",
+    "from __future__ import annotations\n",
+    "\n",
+    "from instamatic import controller\n",
     "from instamatic.formats import write_tiff\n",
     "\n",
-    "ctrl = TEMController.initialize()"
+    "ctrl = controller.initialize()"
    ]
   },
   {

docs/examples/montage_processing.ipynb

@@ -21,9 +21,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from instamatic.montage import *\n",
-    "import numpy as np\n",
+    "from __future__ import annotations\n",
+    "\n",
     "from pathlib import Path\n",
+    "\n",
+    "import numpy as np\n",
+    "\n",
+    "from instamatic.montage import *\n",
+    "\n",
     "np.set_printoptions(suppress=True)\n",
     "\n",
     "# work directory\n",
@@ -88,8 +93,8 @@
    "outputs": [],
    "source": [
     "# Use cross correlation to get difference vectors\n",
-    "m.calculate_difference_vectors(threshold='auto', \n",
-    "                               method='skimage', \n",
+    "m.calculate_difference_vectors(threshold='auto',\n",
+    "                               method='skimage',\n",
     "                               plot=False)\n",
     "\n",
     "# plot the fft_scores\n",
@@ -155,6 +160,7 @@
    "outputs": [],
    "source": [
     "from pyserialem.navigation import sort_nav_items_by_shortest_path\n",
+    "\n",
     "stagecoords = sort_nav_items_by_shortest_path(stagecoords, plot=True);"
    ]
   },
@@ -171,8 +177,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from instamatic import TEMController\n",
-    "ctrl = TEMController.initialize()"
+    "from instamatic import controller\n",
+    "\n",
+    "ctrl = controller.initialize()"
    ]
   },
   {
@@ -228,11 +235,11 @@
     "def acquire_func(ctrl):\n",
     "    # Align to template\n",
     "#     ctrl.align_to(ref_img, apply=True)\n",
-    "    \n",
+    "\n",
     "    # obtain image\n",
-    "    img, h = ctrl.get_image(binsize=binsize)  \n",
+    "    img, h = ctrl.get_image(binsize=binsize)\n",
     "    buffer.append(img)\n",
-    "    \n",
+    "\n",
     "    # store stage position and image somewhere\n",
     "    pos = ctrl.stage.get()\n",
     "    stagepos.append(pos)"
@@ -273,6 +280,7 @@
    "outputs": [],
    "source": [
     "from pyserialem import MapItem, write_nav_file\n",
+    "\n",
     "from instamatic import config\n",
     "\n",
     "# reference image of a centered grid square\n",
@@ -285,7 +293,7 @@
     "buffer = []\n",
     "stagepos = []\n",
     "\n",
-    "   \n",
+    "\n",
     "def write_mrc_stack(fn:str, data: list, overwrite: bool=True, mmap:bool = True):\n",
     "    \"\"\"Write a stack of images to an mrc file.\"\"\"\n",
     "    if mmap:\n",
@@ -301,21 +309,21 @@
     "            f = mrcfile.new(fn, data=data, overwrite=overwrite)\n",
     "        except OSError:\n",
     "            f.close()\n",
-    "    \n",
+    "\n",
     "\n",
     "def post_acquire(ctrl):\n",
     "    fn_nav = work / 'instamatic.nav'\n",
     "    fn_mrc = work / 'mmm.mrc'\n",
-    "    \n",
+    "\n",
     "    write_mrc_stack(fn_mrc, buffer)\n",
-    "    \n",
+    "\n",
     "    items = []\n",
-    "    \n",
+    "\n",
     "    magnification = ctrl.magnification.value\n",
     "    mode = ctrl.mode.get()\n",
     "    mapscalemat = config.calibration[mode]['stagematrix'][magnification]\n",
     "    mapscalemat = [item/binsize for item in mapscalemat]\n",
-    "    \n",
+    "\n",
     "    for i, image in enumerate(buffer):\n",
     "        x, y, z, _, _ = stagepos[i]\n",
     "        shape = image.shape\n",
@@ -334,7 +342,7 @@
     "        items.append(map_item)\n",
     "\n",
     "    write_nav_file(fn_nav, *items)\n",
-    "    \n",
+    "\n",
     "    print(f\"Data saved to `{fn_nav}` and `{fn_mrc}` ({len(buffer)} images)\")"
    ]
   },
@@ -352,8 +360,8 @@
    "outputs": [],
    "source": [
     "sel = stagecoords[0:10]  # Acquire at the first 10 items\n",
-    "ctrl.acquire_at_items(sel, \n",
-    "                      acquire=acquire_func, \n",
+    "ctrl.acquire_at_items(sel,\n",
+    "                      acquire=acquire_func,\n",
     "                      post_acquire=post_acquire)"
    ]
   },

docs/gonio.md

@@ -25,7 +25,7 @@ goniotool_server_host: 'localhost'
 goniotool_server_port: 8090
 ```
 
-The controls are then available in the [`python API`][instamatic.TEMController.TEMController] via [`ctrl.stage`][instamatic.TEMController.stage.Stage] in your own script/notebook:
+The controls are then available in the [`python API`][instamatic.controller] via [`ctrl.stage`][instamatic.microscope.components.Stage] in your own script/notebook:
 
 
 ```python

docs/programs.md

@@ -7,7 +7,7 @@ There are several programs coming with `instamatic`. These docs are autogenerate
 These are the main tools to work with instamatic.
 
 - [instamatic](#instamatic) (`instamatic.main:main`)
-- [instamatic.controller](#instamaticcontroller) (`instamatic.TEMController.TEMController:main_entry`)
+- [instamatic.controller](#instamaticcontroller) (`instamatic.controller:main_entry`)
 
 **Experiments**
 

docs/tem_api.md

@@ -7,8 +7,8 @@ The TEMController is at the heart of `instamatic`. Every routine depends on acce
 In IPython/Jupyter:
 
 ```python
-from instamatic import TEMController
-ctrl = TEMController.initialize()
+from instamatic import controller
+ctrl = controller.initialize()
 ```
 
 If no names for the camera/microscope are given, it reads the defaults from the config directory listed when TEMController is imported (`config/settings.yaml`). The config directory is generated on the first run of `instamatic`. By default these are set to load simulation of the camera/microscope. The simulation is is a good test to see if it works at all (a shortcut to this is to type `instamatic.controller.exe` in the terminal).
@@ -18,20 +18,20 @@ The config files work as follows: The global configurations are defined in `conf
 You can override the defaults here, so on the microscope computer you could try:
 
 ```python
-ctrl = TEMController.initialize(tem_name='jeol', cam_name='timepix', stream=True)
+ctrl = controller.initialize(tem_name='jeol', cam_name='timepix', stream=True)
 ```
 
 `stream` indicates that the camera can be streamed (like the timepix camera). Other cameras, like the gatan (orius/ultrascan) cameras communicate through DigitalMicrograph, and can therefore not be streamed. Instead the live stream can be shown in DM, and therefore needs DM to be open.
 
 Otherwise, to skip camera initialization:
 
 ```python
-ctrl = TEMController.initialize(tem_name='jeol', cam_name=None)
+ctrl = controller.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?`).
+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. `controller.initialize?`).
 
-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/`
+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/microscope/interface`
 
 The `ctrl` object allows full control over the electron microscope. For example, to read out the position of the sample stage:
 ```python
@@ -250,9 +250,9 @@ An example rotation experiment could look something like this:
 
 ```python
 from instamatic.formats import write_tiff
-from instamatic import TEMController
+from instamatic import controller
 
-ctrl = TEMController.initialize()
+ctrl = controller.initialize()
 
 exposure_time = 1.0
 angles = range(-40, 40, 1)

mkdocs.yml

@@ -17,11 +17,11 @@ nav:
   - network.md
   - Python API:
     - instamatic.TEMController:
-      - TEMController: api/TEMController_TEMController.md
-      - Deflectors: api/TEMController_deflectors.md
-      - Lenses: api/TEMController_lenses.md
-      - States: api/TEMController_states.md
-      - Stage: api/TEMController_stage.md
+      - TEMController: api/controller.md
+      - Deflectors: api/components_deflectors.md
+      - Lenses: api/components_lenses.md
+      - States: api/components_states.md
+      - Stage: api/components_stage.md
     - instamatic.tools: api/instamatic_tools.md
     - instamatic.montage: api/instamatic_montage.md
     - instamatic.gridmontage: api/instamatic_gridmontage.md

pyproject.toml

@@ -90,7 +90,7 @@ publishing = [
 
 [project.scripts]
 "instamatic" = "instamatic.main:main"
-"instamatic.controller" = "instamatic.TEMController.TEMController:main_entry"
+"instamatic.controller" = "instamatic.controller:main_entry"
 # experiments
 "instamatic.serialed" = "instamatic.experiments.serialed.experiment:main"
 "instamatic.camera" = "instamatic.camera.camera:main_entry"

readme.md

@@ -79,13 +79,13 @@ Alternatively, some of the methods implemented in `Instamatic` are described in:
 * **`docs/`** - Documentation
 * **`src/`** - Source code for instamatic
 * **`src/instamatic/`**
-  * **`TEMController/`** - Microscope interaction code
   * **`calibrate/`** - Tools for calibration
   * **`camera/`** - Camera interaction code
   * **`config/`** - Configuration management
   * **`experiments/`** - Specific data collection routines
   * **`formats/`** - Image formats and other IO
   * **`gui/`** - GUI code
+  * **`microscope/`** - Microscope interaction code
   * **`neural_network/`** - Crystal quality prediction
   * **`processing/`** - Data processing tools
   * **`server/`** - Manages interprocess/network communication
@@ -94,6 +94,7 @@ Alternatively, some of the methods implemented in `Instamatic` are described in:
   * **`admin.py`** - Check for administrator
   * **`banner.py`** - Appropriately annoying thank you message
   * **`browser.py`** - Montage browsing class
+  * **`controller.py`** - Main instrument interaction code
   * **`exceptions.py`** - Internal exceptions
   * **`goniotool.py`** - Goniotool (JEOL) interaction code
   * **`gridmontage.py`** - Grid montage data collection code