Merge branch 'main' into formatting-and-documentation

Author: stefsmeets

.github/workflows/test.yml

@@ -17,6 +17,7 @@ on:
 jobs:
   build:
     runs-on: windows-latest
+    if: github.event.pull_request.draft == false
 
     strategy:
       fail-fast: false

docs/config.md

@@ -271,14 +271,18 @@ This file holds all the specifications of the microscope as necessary. It is imp
 **ranges**
 : In the child items, all the magnification ranges must be defined. They can be obtained through the API using: `ctrl.magnification.get_ranges()`. This will step through all the magnifications and return them as a dictionary.
 
-**range/diff**
+**ranges/diff**
 : List here the available camera lengths available on the microscope in ascending order:
 ```yaml
 ranges:
   diff: [150, 200, 250, 300, 400, 500, 600, 800, 1000,
     1200, 1500, 2000, 2500, 3000, 3500, 4000, 4500]
 ```
 
+!!! note
+
+    For FEI/TFS machines, use `range/D` instead of `ranges/diff`.
+
 **ranges/mag**
 : Here, mag must be one of the known mag ranges, i.e. `lowmag`, `mag1`, `samag`. What follows is a list of all available magnifications on the microscope in ascending order, for example:
 ```yaml
@@ -289,3 +293,7 @@ ranges:
     400000, 500000, 600000, 800000, 1000000, 1200000,
     1500000, 2000000]
 ```
+
+!!! note
+
+    For FEI/TFS machines, the ranges are instead set as: `LM` (lowmag), `Mi` (low/intermediate mag), `SA` (high mag), `Mh` (highest mag), and `D` (diffraction mode).

docs/setup.md

@@ -35,7 +35,7 @@ In order of priority:
    In `config/settings.yaml` define the camera interface you want to use. You can use the autoconfig tool or one of the example files and modify those. You can name these files anything you want, as long as the name under `microscope` matches the filename in `config/microscope`
 
 ### __3. Set up the magnifications and camera lengths__  
-   In the config file, i.e `config/microscope/jeol.yaml`, set the correct camera lengths (`range_diff`) and magnifications for your microscopes (`range_lowmag` and `range_mag1`). Also make sure you set the wavelength. Again, the autoconfig tool is your best friend, otherwise, the way to get those numbers is to simply write them down as you turn the magnification knob on the microcope.
+   In the config file, i.e `config/microscope/jeol.yaml`, set the correct camera lengths (`ranges/diff`) and magnifications for your microscopes (`ranges/lowmag` and `ranges/mag1`). Also make sure you set the wavelength. Again, the autoconfig tool is your best friend, otherwise, the way to get those numbers is to simply write them down as you turn the magnification knob on the microcope.
 
 ### __4. Set up the camera interface__  
    Specify the file you want to use for the camera interface, i.e. `camera: timepix` points to `config/camera/timepix.yaml`. In this file, make sure that the interface is set to your camera type and update the numbers as specified in the config documentation. If you do not want to set up the camera interface at this moment, you can use `camera: simulate` to fake the camera connection.

instamatic/TEMController/fei_microscope.py

@@ -28,95 +28,21 @@
 # 0.02: 0.593
 # 0.01: 0.297
 
-
 FUNCTION_MODES = {0: 'LM', 1: 'Mi', 2: 'SA', 3: 'Mh', 4: 'LAD', 5: 'D'}
 
-MagnificationMapping = {
-    1: 45,
-    2: 58,
-    3: 73,
-    4: 89,
-    5: 115,
-    6: 145,
-    7: 185,
-    8: 235,
-    9: 300,
-    10: 380,
-    11: 470,
-    12: 600,
-    13: 760,
-    14: 950,
-    15: 1200,
-    16: 1550,
-    17: 3400,
-    18: 4400,
-    19: 5600,
-    20: 7200,
-    21: 8800,
-    22: 11500,
-    23: 14500,
-    24: 18500,
-    25: 24000,
-    26: 30000,
-    27: 38000,
-    28: 49000,
-    29: 61000,
-    30: 77000,
-    31: 100000,
-    32: 130000,
-    33: 165000,
-    34: 215000,
-    35: 265000,
-    36: 340000,
-    37: 430000,
-    38: 550000,
-    39: 700000,
-    40: 890000,
-    41: 1150000,
-    42: 1250000,
-    43: 960000,
-    44: 750000,
-    45: 600000,
-    46: 470000,
-    47: 360000,
-    48: 285000,
-    49: 225000,
-    50: 175000,
-    51: 145000,
-    52: 115000,
-    53: 89000,
-    54: 66000,
-    55: 52000,
-    56: 41000,
-    57: 32000,
-    58: 26000,
-    59: 21000,
-    60: 8300,
-    61: 6200,
-    62: 3100}
-
-CameraLengthMapping = {
-    1: 34,
-    2: 42,
-    3: 53,
-    4: 68,
-    5: 90,
-    6: 115,
-    7: 140,
-    8: 175,
-    9: 215,
-    10: 265,
-    11: 330,
-    12: 420,
-    13: 530,
-    14: 680,
-    15: 830,
-    16: 1050,
-    17: 1350,
-    18: 1700,
-    19: 2100,
-    20: 2700,
-    21: 3700}
+
+def get_magnification_mapping():
+    functions = ('LM', 'Mi', 'SA', 'Mh')
+    values = (val for function in functions for val in config.microscope.ranges[function])
+    return {num + 1: val for num, val in enumerate(values)}
+
+
+def get_camera_length_mapping():
+    return {num + 1: val for num, val in enumerate(config.microscope.ranges['D'])}
+
+
+MagnificationMapping = get_magnification_mapping()
+CameraLengthMapping = get_camera_length_mapping()
 
 
 class FEIMicroscope:

instamatic/camera/camera_merlin.py

@@ -47,6 +47,7 @@ def MPX_CMD(type_cmd: str = 'GET', cmd: str = 'DETECTORSTATUS') -> bytes:
 class CameraMerlin:
     """Camera interface for the Quantum Detectors Merlin camera."""
     START_SIZE = 14
+    MAX_NUMFRAMESTOACQUIRE = 42_949_672_950
 
     def __init__(self, name='merlin'):
         """Initialize camera module."""
@@ -161,12 +162,12 @@ def setup_soft_trigger(self, exposure: float = None):
 
         self._frame_number = 0
 
-        # Set NUMFRAMESTOACQUIRE to a large number
-        # Merlin will only collect this number of frames with SOFTTRIGGER
-        self.merlin_set('NUMFRAMESTOACQUIRE', 10_000)
+        # Set NUMFRAMESTOACQUIRE to maximum
+        # Merlin collects up to this number of frames with a single SOFTTRIGGER acquisition
+        self.merlin_set('NUMFRAMESTOACQUIRE', self.MAX_NUMFRAMESTOACQUIRE)
 
-        self.merlin_set('TRIGGERSTART', '5')
-        self.merlin_set('NUMFRAMESPERTRIGGER', '1')
+        self.merlin_set('TRIGGERSTART', 5)
+        self.merlin_set('NUMFRAMESPERTRIGGER', 1)
         self.merlin_cmd('STARTACQUISITION')
 
         start = self.receive_data(nbytes=self.START_SIZE)
@@ -203,7 +204,10 @@ def getImage(self, exposure: float = None, **kwargs) -> np.ndarray:
             self.setup_soft_trigger(exposure=exposure)
         elif exposure != self._soft_trigger_exposure:
             logger.info('Change exposure to %s s', exposure)
-            self.teardown_soft_trigger()
+            self.setup_soft_trigger(exposure=exposure)
+        elif self._frame_number == self.MAX_NUMFRAMESTOACQUIRE:
+            logger.debug(('Maximum frame number reached for this acquisition, '
+                          'resetting soft trigger.') % self.MAX_NUMFRAMESTOACQUIRE)
             self.setup_soft_trigger(exposure=exposure)
 
         self.merlin_cmd('SOFTTRIGGER')

instamatic/config/autoconfig.py

@@ -191,9 +191,11 @@ def main():
     if cam_config:
         print(f'    camera: {cam_name}_cam')
     print()
-    print(f'Todo: Check and update the pixelsizes in `{calib_config_fn}`')
-    print('    In real space, pixelsize in nm')
-    print('    In reciprocal space, pixelsize in px/Angstrom')
+    print('Todo:')
+    print(f' 1. Check and update the pixelsizes in `{calib_config_fn}`')
+    print('    - In real space, pixelsize in nm')
+    print('    - In reciprocal space, pixelsize in px/Angstrom')
+    print(f' 2. Check and update magnification ranges in `{microscope_config_fn}`')
 
 
 if __name__ == '__main__':

instamatic/config/microscope/fei_simu.yaml

@@ -1,10 +1,9 @@
 interface: fei_simu
 ranges:
-  diff: [150, 200, 250, 300, 400, 500, 600, 800, 1000, 1200, 1500, 2000, 2500, 3000,
-    3500, 4000, 4500]
-  lowmag: [50, 80, 100, 150, 200, 250, 300, 400, 500, 600, 800, 1000, 1200, 1500,
-    2000, 2500, 3000, 5000, 6000, 8000, 10000, 12000, 15000]
-  mag1: [2500, 3000, 4000, 5000, 6000, 8000, 10000, 12000, 15000, 20000, 25000, 30000,
-    40000, 50000, 60000, 80000, 100000, 120000, 150000, 200000, 250000, 300000, 400000,
-    500000, 600000, 800000, 1000000, 1500000, 2000000]
+  LM: [45, 58, 73, 89, 115, 145, 185, 235, 300, 380, 470, 600, 760, 950, 1200, 1550]
+  Mi: []
+  SA: [3400, 4400, 5600, 7200, 8800, 11500, 14500, 18500, 24000, 30000, 38000, 49000, 61000, 77000, 100000, 130000, 165000, 215000, 265000, 340000]
+  Mh: [430000, 550000, 700000, 890000, 1150000, 1250000, 960000, 750000, 600000, 470000, 360000, 285000, 225000, 175000, 145000, 115000, 89000, 66000, 52000, 41000, 32000, 26000, 21000, 8300, 6200, 3100]
+  D: [34, 42, 53, 68, 90, 115, 140, 175, 215, 265, 330, 420, 530, 680, 830, 1050, 1350, 1700, 2100, 2700, 3700]
+  LAD: []
 wavelength: 0.019687

instamatic/config/microscope/fei_themisZ.yaml

@@ -1,10 +1,8 @@
 interface: fei
 ranges:
-  diff: [150, 200, 250, 300, 400, 500, 600, 800, 1000, 1200, 1500, 2000, 2500, 3000,
-    3500, 4000, 4500]
-  lowmag: [50, 80, 100, 150, 200, 250, 300, 400, 500, 600, 800, 1000, 1200, 1500,
-    2000, 2500, 3000, 5000, 6000, 8000, 10000, 12000, 15000]
-  mag1: [2500, 3000, 4000, 5000, 6000, 8000, 10000, 12000, 15000, 20000, 25000, 30000,
-    40000, 50000, 60000, 80000, 100000, 120000, 150000, 200000, 250000, 300000, 400000,
-    500000, 600000, 800000, 1000000, 1500000, 2000000]
+  LM: [45, 58, 73, 89, 115, 145, 185, 235, 300, 380, 470, 600, 760, 950, 1200, 1550]
+  Mi: []
+  SA: [3400, 4400, 5600, 7200, 8800, 11500, 14500, 18500, 24000, 30000, 38000, 49000, 61000, 77000, 100000, 130000, 165000, 215000, 265000, 340000]
+  Mh: [430000, 550000, 700000, 890000, 1150000, 1250000, 960000, 750000, 600000, 470000, 360000, 285000, 225000, 175000, 145000, 115000, 89000, 66000, 52000, 41000, 32000, 26000, 21000, 8300, 6200, 3100]
+  D: [34, 42, 53, 68, 90, 115, 140, 175, 215, 265, 330, 420, 530, 680, 830, 1050, 1350, 1700, 2100, 2700, 3700]
 wavelength: 0.019687