Merge pull request #251 from DeMarcoLab/v0.2-dev

v0.2.4 Release

.gitignore

@@ -55,3 +55,4 @@ scratch/tile-images/*
 fibsem/log/*
 fibsem/db/fibsem.db
 fibsem/notebook.ipynb
+scratch/health-monitor/*

docs/started.md

@@ -5,6 +5,10 @@
 
 Please see README.md
 
+### Desktop Shortcut
+
+To create a desktop shortcut for FibsemUI, simply run the shortcut.py file.
+
 ### System Configuration
 
 The system configuration is defined by a system.yaml file. This defines various system settings, including connection details, beam, imaging, and stage settings. 

external/application_files/autolamella.xml

@@ -0,0 +1,72 @@
+<Content Version="Fei ApplicationFile 1.1">
+
+    <!-- Application file for milling silicon (Si) without any gas for Xe PFIB -->
+
+
+    <!-- Client tag determines where file is displayed to user. 
+         Can be XTUI, iFast or a combination separated by comma -->
+    <Client xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="string">
+	XTUI, iFast
+    </Client >
+
+
+    <!-- Beam, must be Electron or Ion -->
+    <Beam xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="string">
+	Ion
+    </Beam>
+
+
+    <!-- Pattern filter sets if file will be displayed for a given pattern type.
+         Can be set to Line, Circle, Rectangle, CCS, RCS, Bitmap, StreamFile, Polygon
+         Can be a combination separated by comma(s) -->
+    <PatternType xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="string">
+	Line, Circle, Rectangle, Bitmap, Streamfile, Polygon, CCS, RCS
+    </PatternType>
+
+
+    <!-- Gas type, must match name of gas in UI or empty for no gas -->
+    <GasType xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="string">
+    </GasType>
+
+
+    <!-- Dwell time per point, in seconds, minimum is 50e-9 (50ns), maximum is 4.5e-3 (4.5 ms) -->
+    <DwellTime xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="r8">
+        1.000E-6
+    </DwellTime>
+
+
+    <!-- Overlap between points as percentage of the spot diameter. Must be < 100%. -->
+    <Overlap xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="r8">
+	98
+    </Overlap>
+
+
+    <!-- Volume per Dose, the volume of material that is deposited or removed per dose of the beam in m^3/Coulomb.
+         1e-9 m^3/C = 1 um^3/nC. (Si) is 0.27 um^3/nc = 0.27e-9 m^3/C -->
+    <VolumePerDose xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="r8">
+        0.00000000038
+    </VolumePerDose>
+
+
+    <!-- Blur and Defocus.  
+         Blur- the additional beam diameter that is caused by defocussing in m. 
+         Note that the total beam diameter is the root of the sum of the 
+         squared beam, interaction and blur diameters.
+         
+         Defocus- Defocus the beam in m to longer or shorter working distance while patterning.
+         Positive values will set focus value to a longer working distance.
+         Negative values will set focus value to a shorter working distance.
+
+         Only use a Blur or a Defocus value.  Do not use both.
+         If no value is to be set for patterning a Blur or Defocus must be set to a 0 -->
+    <Blur xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="r8">
+        0
+    </Blur>
+
+
+    <!-- Relative Interaction Diameter must always be set to 0. -->
+    <RelativeInteractionDiameter xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="r8">
+        0
+    </RelativeInteractionDiameter>
+
+</Content> 

external/application_files/cryo_Pt_dep.xml

@@ -0,0 +1,16 @@
+<Content Version="Fei ApplicationFile 1.1" xmlns:dt="urn:schemas-microsoft-com:datatypes">
+  <PatternType dt:dt="string">Line</PatternType>
+  <Beam dt:dt="string">Electron</Beam>
+  <GasType dt:dt="string">Pt cryo</GasType>
+  <GasDutyCycle dt:dt="string">1:0.2</GasDutyCycle>
+  <GasNeedlePosition dt:dt="string">1:cryo</GasNeedlePosition>
+  <DwellTime dt:dt="r8">1E-07</DwellTime>
+  <Overlap dt:dt="r8">-90</Overlap>
+  <VolumePerDose dt:dt="r8">5E-11</VolumePerDose>
+  <SaturationSputterRate dt:dt="r8">0</SaturationSputterRate>
+  <RefreshTime dt:dt="r8">0</RefreshTime>
+  <Defocus dt:dt="r8">0</Defocus>
+  <InteractionDiameter dt:dt="r8">0</InteractionDiameter>
+  <MaximumDosePerArea dt:dt="r8">0</MaximumDosePerArea>
+  <SaturationCurrentDensity dt:dt="r8">1</SaturationCurrentDensity>
+</Content>

fibsem/config.py

@@ -1,4 +1,4 @@
-METADATA_VERSION = "v1"
+METADATA_VERSION = "v2"
 
 # sputtering rates, from microscope application files
 MILLING_SPUTTER_RATE = {
@@ -35,6 +35,11 @@
 REFERENCE_HFW_SUPER = 80e-6
 REFERENCE_HFW_ULTRA = 50e-6
 
+REFERENCE_RES_SQUARE = [1024, 1024]
+REFERENCE_RES_LOW = [768, 512]
+REFERENCE_RES_MEDIUM = [1536, 1024]
+REFERENCE_RES_HIGH = [3072, 2048]
+REFERENCE_RES_SUPER = [6144, 4096]
 
 MILL_HFW_THRESHOLD = 0.005 # 0.5% of the image 
 

fibsem/config/protocol.yaml

@@ -121,5 +121,14 @@ patterns:
     thickness: 2.0e-6
     radius: 10.0e-6
     depth: 1.0e-6  
-
+  Trapezoid:
+    inner_width: 10.0e-6
+    outer_width: 20.0e-6
+    trench_height: 5.0e-6
+    depth: 1.0e-6
+    distance: 1.0e-6
+    n_rectangles: 10
+    overlap: 0.0
+    scan_direction: "ToptoBottom"
+    type: "Trapezoid"
 

fibsem/detection/detection.py

@@ -140,6 +140,7 @@ class LandingPost(Feature):
 
     def detect(self, img: np.ndarray, mask: np.ndarray = None, point:Point=None) -> 'LandingPost':
         self.px = detect_landing_post_v4(mask, point)
+        # self.px = detect_landing_post_v3(img, landing_pt=None)
         return self.px