Add aperture and new capabilities for linking controls.

[Brow71189]

Most important cahnges:

• Add aperture that can be moved and "distorted" (i.e. dipole and quadropole effect simulation)
• Add functions to 'Instrument' that facilitate adding new inputs to existing controls
• Allow input weights for controls to be controls in addition to float
• Add option to attach a python expression as control input (only one expression per control can be set, but it can be arbitrarily complex)

This might fix #11 and #17 (or at least work towards fixing them)

[Brow71189]

Forgot one item:

• Changed meaning of convergence angle to reflect its real meaning (in the simulator it only controls the size of the aperture on the ronchigram camera, the effect on the scan is not simulated yet)

[cmeyer]

This looks good so far. Is it still a work in progress? (if so, change title to have [WIP] at the end)

Also, any affect on performance for the regular acquisition cases?

[cmeyer]

Also: can you update the CHANGES file?

[Brow71189]

Also: can you update the CHANGES file?

Done.

[Brow71189]

This looks good so far. Is it still a work in progress? (if so, change title to have [WIP] at the end)

Also, any affect on performance for the regular acquisition cases?

I didn't measure it but also don't see any immediate effects. Adding the aperture will add a little bit of computational time, but that happens only when you actually "insert" it. And still it is probably negligible compared to the overall simlation time.
Making the simulator (especially for the amorphous sample) faster would be nice thing though. Maybe I'll work on that sometimes in the near future.

[cmeyer]

How about this to make the flake look the same:

diff --git a/nionswift_plugin/usim/InstrumentDevice.py b/nionswift_plugin/usim/InstrumentDevice.py
index adf85cc..0308606 100755
--- a/nionswift_plugin/usim/InstrumentDevice.py
+++ b/nionswift_plugin/usim/InstrumentDevice.py
@@ -350,13 +350,15 @@ class Instrument(stem_controller.STEMController):
         self.instrument_id = instrument_id
         self.property_changed_event = Event.Event()
         self.__camera_frame_event = threading.Event()
-        self.__samples = [SampleSimulator.RectangleFlakeSample(), SampleSimulator.AmorphousSample()]
-        self.__sample_index = 1
 
         # define the STEM geometry limits
         self.stage_size_nm = 1000
         self.max_defocus = 5000 / 1E9
 
+        # define the samples
+        self.__samples = [SampleSimulator.RectangleFlakeSample(self.stage_size_nm), SampleSimulator.AmorphousSample()]
+        self.__sample_index = 0
+
         self.__stage_position_m = Geometry.FloatPoint()
         self.__slit_in = False
         self.__energy_per_channel_eV = 0.5
diff --git a/nionswift_plugin/usim/SampleSimulator.py b/nionswift_plugin/usim/SampleSimulator.py
index 6444312..8be0e9e 100644
--- a/nionswift_plugin/usim/SampleSimulator.py
+++ b/nionswift_plugin/usim/SampleSimulator.py
@@ -84,9 +84,9 @@ class Sample(abc.ABC):
 
 class RectangleFlakeSample:
 
-    def __init__(self):
+    def __init__(self, stage_size_nm: float):
         self.__features = list()
-        sample_size_m = Geometry.FloatSize(height=20, width=20) / 1E9
+        sample_size_m = Geometry.FloatSize(height=20 * stage_size_nm / 100, width=20 * stage_size_nm / 100) / 1E9
         feature_percentage = 0.3
         random_state = random.getstate()
         random.seed(1)
diff --git a/nionswift_plugin/usim/ScanDevice.py b/nionswift_plugin/usim/ScanDevice.py
index d77b628..4c04935 100644
--- a/nionswift_plugin/usim/ScanDevice.py
+++ b/nionswift_plugin/usim/ScanDevice.py
@@ -68,9 +68,9 @@ class Device:
         # profiles.append(scan_base.ScanFrameParameters({"size": (512, 512), "pixel_time_us": 0.2}))
         # profiles.append(scan_base.ScanFrameParameters({"size": (1024, 1024), "pixel_time_us": 0.2}))
         # profiles.append(scan_base.ScanFrameParameters({"size": (2048, 2048), "pixel_time_us": 2.5}))
-        profiles.append(scan_base.ScanFrameParameters({"size": (256, 256), "pixel_time_us": 1, "fov_nm": 10}))
-        profiles.append(scan_base.ScanFrameParameters({"size": (512, 512), "pixel_time_us": 1, "fov_nm": 40}))
-        profiles.append(scan_base.ScanFrameParameters({"size": (1024, 1024), "pixel_time_us": 1, "fov_nm": 100}))
+        profiles.append(scan_base.ScanFrameParameters({"size": (256, 256), "pixel_time_us": 1, "fov_nm": self.__instrument.stage_size_nm * 0.1}))
+        profiles.append(scan_base.ScanFrameParameters({"size": (512, 512), "pixel_time_us": 1, "fov_nm": self.__instrument.stage_size_nm * 0.4}))
+        profiles.append(scan_base.ScanFrameParameters({"size": (1024, 1024), "pixel_time_us": 1, "fov_nm": self.__instrument.stage_size_nm * 1.0}))
         return profiles
 
     @property

[Brow71189]

How about this to make the flake look the same:

diff --git a/nionswift_plugin/usim/InstrumentDevice.py b/nionswift_plugin/usim/InstrumentDevice.py
index adf85cc..0308606 100755
--- a/nionswift_plugin/usim/InstrumentDevice.py
+++ b/nionswift_plugin/usim/InstrumentDevice.py
@@ -350,13 +350,15 @@ class Instrument(stem_controller.STEMController):
         self.instrument_id = instrument_id
         self.property_changed_event = Event.Event()
         self.__camera_frame_event = threading.Event()
-        self.__samples = [SampleSimulator.RectangleFlakeSample(), SampleSimulator.AmorphousSample()]
-        self.__sample_index = 1
 
         # define the STEM geometry limits
         self.stage_size_nm = 1000
         self.max_defocus = 5000 / 1E9
 
+        # define the samples
+        self.__samples = [SampleSimulator.RectangleFlakeSample(self.stage_size_nm), SampleSimulator.AmorphousSample()]
+        self.__sample_index = 0
+
         self.__stage_position_m = Geometry.FloatPoint()
         self.__slit_in = False
         self.__energy_per_channel_eV = 0.5
diff --git a/nionswift_plugin/usim/SampleSimulator.py b/nionswift_plugin/usim/SampleSimulator.py
index 6444312..8be0e9e 100644
--- a/nionswift_plugin/usim/SampleSimulator.py
+++ b/nionswift_plugin/usim/SampleSimulator.py
@@ -84,9 +84,9 @@ class Sample(abc.ABC):
 
 class RectangleFlakeSample:
 
-    def __init__(self):
+    def __init__(self, stage_size_nm: float):
         self.__features = list()
-        sample_size_m = Geometry.FloatSize(height=20, width=20) / 1E9
+        sample_size_m = Geometry.FloatSize(height=20 * stage_size_nm / 100, width=20 * stage_size_nm / 100) / 1E9
         feature_percentage = 0.3
         random_state = random.getstate()
         random.seed(1)
diff --git a/nionswift_plugin/usim/ScanDevice.py b/nionswift_plugin/usim/ScanDevice.py
index d77b628..4c04935 100644
--- a/nionswift_plugin/usim/ScanDevice.py
+++ b/nionswift_plugin/usim/ScanDevice.py
@@ -68,9 +68,9 @@ class Device:
         # profiles.append(scan_base.ScanFrameParameters({"size": (512, 512), "pixel_time_us": 0.2}))
         # profiles.append(scan_base.ScanFrameParameters({"size": (1024, 1024), "pixel_time_us": 0.2}))
         # profiles.append(scan_base.ScanFrameParameters({"size": (2048, 2048), "pixel_time_us": 2.5}))
-        profiles.append(scan_base.ScanFrameParameters({"size": (256, 256), "pixel_time_us": 1, "fov_nm": 10}))
-        profiles.append(scan_base.ScanFrameParameters({"size": (512, 512), "pixel_time_us": 1, "fov_nm": 40}))
-        profiles.append(scan_base.ScanFrameParameters({"size": (1024, 1024), "pixel_time_us": 1, "fov_nm": 100}))
+        profiles.append(scan_base.ScanFrameParameters({"size": (256, 256), "pixel_time_us": 1, "fov_nm": self.__instrument.stage_size_nm * 0.1}))
+        profiles.append(scan_base.ScanFrameParameters({"size": (512, 512), "pixel_time_us": 1, "fov_nm": self.__instrument.stage_size_nm * 0.4}))
+        profiles.append(scan_base.ScanFrameParameters({"size": (1024, 1024), "pixel_time_us": 1, "fov_nm": self.__instrument.stage_size_nm * 1.0}))
         return profiles
 
     @property

Looks good.

[cmeyer]

Merged e5ef7f9..d00d1b2