Merge pull request #7 from azazellochg/devel

0.9.5

.github/workflows/publish_and_tag.yml

@@ -18,7 +18,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install setuptools twine
         pip install numpy scipy matplotlib mrcfile
-    - name: Build and publish
+    - name: Publish
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

CHANGES.txt

@@ -1,3 +1,11 @@
+0.9.5:
+    - afis # of checks reduced to 4
+    - added frame alignment with SEM plugin, enabled for Young fringes and gold diffraction tests
+    - configs updated
+    - reset img shifts at the start
+    - skip auto-stigmate very close to focus, because SEM will increase the defocus
+    - add wait for drift for eucentricity and tilt axis tests
+    - add simple GUI as an option
 0.9.4:
     - add atlas realignment test
     - update Delay command

README.rst

@@ -69,21 +69,22 @@ Offline installation
 Available scripts
 -----------------
 
-- AFIS
+- AFIS validation
     - Specification (Krios): coma < 750 nm, astigmatism < 10 nm for 5 um shift. Glacios: coma < 1200 nm, astigmatism < 15 nm for 6 um shift
     - Description: Measure residual beam tilt and astigmatism at different image shift positions while EPU is open.
 - Atlas realignment
+    - Specification: none
     - Description: Compare the shift and rotation between two atlases acquired when reloading the same grid.
 - Magnification anisotropy
     - Specification: <1%
     - Description: Acquire a defocus series and plot astigmatism versus defocus. Calculate anisotropy by estimating deviation from linear behaviour.
 - C2 Fresnel fringes
     - Specification: on FFI system there should be <5 fringes at 96 kx in nanoprobe close to focus
     - Description: Take a picture of a flood beam to see if the fringes from C2 aperture extend all the way to the center (non-FFI systems).
-- Eucentricity
+- Eucentricity check
     - Specification: <2 um in X/Y, <4 um defocus (Krios G2, G3, G3i)
     - Description: Estimate X,Y and defocus offset while tilting the stage.
-- Gain reference
+- Gain reference check
     - Specification: none
     - Description: Take a picture of a flood beam and check the auto-correlation image.
 - Gold diffraction
@@ -115,3 +116,11 @@ First, have a look at **config.py**: edit *microscopes* dictionary and individua
 .. code-block:: python
 
     perfectem
+
+If you prefer clicking buttons over console, you can create a desktop script **PerfectEM.bat** that contains one line:
+
+.. code-block::
+
+    perfectem-gui
+
+PS. The simple GUI requires Python built with tkinter support.

perfectem/__init__.py

@@ -1,3 +1,5 @@
+#!python
+# -*- coding: utf-8 -*-
 # **************************************************************************
 # *
 # * Authors:     Grigory Sharov ([email protected]) [1]
@@ -30,38 +32,39 @@
 
 from .config import microscopes
 
-__version__ = '0.9.4'
+__version__ = '0.9.5'
 
-tests = (
-    ("AFIS", "AFIS validation"),
-    ("Anisotropy", "Magnification anisotropy"),
-    ("C2Fringes", "C2 Fresnel fringes"),
-    ("Eucentricity", "Eucentricity check"),
-    ("GainRef", "Gain reference check"),
-    ("GoldDiffr", "Gold diffraction"),
-    ("InfoLimit", "Information limit (Young fringes)"),
-    ("PointRes", "Point resolution"),
-    ("StageDrift", "Stage drift"),
-    ("ThonRings", "Thon rings"),
-    ("TiltAxis", "Tilt axis offset"),
-)
+tests = {
+    "AFIS": "AFIS validation",
+    "AtlasRealignment": "Atlas realignment",
+    "Anisotropy": "Magnification anisotropy",
+    "C2Fringes": "C2 Fresnel fringes",
+    "Eucentricity": "Eucentricity check",
+    "GainRef": "Gain reference check",
+    "GoldDiffr": "Gold diffraction",
+    "InfoLimit": "Information limit",
+    "PointRes": "Point resolution",
+    "StageDrift": "Stage drift",
+    "ThonRings": "Thon rings",
+    "TiltAxis": "Tilt axis offset"
+}
 
 
 def show_all_tests(print_docstr: bool = False) -> None:
     """ Print list of tests, with an optional docstring for each. """
-    for num, test in enumerate(tests, start=1):
-        print(f"\t[{num}] {test[1]}")
+    for i, item in enumerate(tests.items()):
+        print(f"\t[{i+1}] {item[1]}")
         if print_docstr:
             module = importlib.import_module("perfectem.scripts")
-            func = getattr(module, test[0])
+            func = getattr(module, item[0])
             print(func.__doc__)
             print("="*80)
 
 
 def main(argv: Optional[List] = None) -> None:
     try:
         import serialem
-    except ImportError:
+    except ModuleNotFoundError:
         raise ImportError("This program must be run on the computer with SerialEM Python module")
 
     parser = argparse.ArgumentParser(description="This script launches selected TEM performance test")
@@ -79,16 +82,23 @@ def main(argv: Optional[List] = None) -> None:
             raise IndexError("Wrong test number!")
 
         print("\nAvailable microscopes:")
-        for scope_num, scope in enumerate(microscopes, start=1):
-            print(f"\t[{scope_num}] {scope[0]}")
+        for scope_num, scope in enumerate(microscopes.keys(), start=1):
+            print(f"\t[{scope_num}] {scope}")
 
         scope_num = int(input("\nInput the microscope number: ").strip()) - 1
         if scope_num not in range(len(microscopes)):
             raise IndexError("Wrong microscope number!")
-        scope_name = microscopes[scope_num][0]
+        scope_name = list(microscopes.keys())[scope_num]
 
-        func_name = tests[test_num][0]
+        func_name = list(tests.keys())[test_num]
         module = importlib.import_module("perfectem.scripts")
         func_object = getattr(module, func_name)
         print(func_object.__doc__)
-        func_object(scope_name=scope_name, **microscopes[scope_num][1][func_name]).run()
+        func_args = list(microscopes.values())[scope_num][func_name]
+        func_object(scope_name=scope_name, **func_args).run()
+
+
+def main_gui() -> None:
+    from .gui import Application
+    gui = Application(tests, microscopes)
+    gui.create_widgets()

perfectem/common.py

@@ -39,7 +39,8 @@
 class BaseSetup:
     """ Initialization and common functions. """
 
-    def __init__(self, log_fn: str, scope_name: str, **kwargs: Any) -> None:
+    def __init__(self, log_fn: str, scope_name: str,
+                 camera_num: Optional[int] = None, **kwargs: Any) -> None:
         """ Setup logger, camera settings and common SerialEM params. """
 
         sem.ConnectToSEM(SERIALEM_PORT, SERIALEM_IP)
@@ -48,7 +49,7 @@ def __init__(self, log_fn: str, scope_name: str, **kwargs: Any) -> None:
         self.SCOPE_HAS_C3 = self.func_is_implemented("ReportIlluminatedArea")
         self.SCOPE_HAS_AUTOFILL = self.func_is_implemented("AreDewarsFilling")
         self.SCOPE_HAS_APER_CTRL = self.func_is_implemented("ReportApertureSize", 1)
-        self.CAMERA_NUM = 1
+        self.CAMERA_NUM = camera_num or 1
         self.CAMERA_HAS_DIVIDEBY2 = False
         self.CAMERA_MODE = 0  # linear
         self.DELAY = 3
@@ -60,7 +61,7 @@ def __init__(self, log_fn: str, scope_name: str, **kwargs: Any) -> None:
                      f"hasAutofill={self.SCOPE_HAS_AUTOFILL}, "
                      f"hasApertureControl={self.SCOPE_HAS_APER_CTRL}")
 
-        self.select_camera()
+        self.select_camera(camera_num)
 
         sem.ClearPersistentVars()
         sem.SetUserSetting("DriftProtection", 1, 1)
@@ -101,40 +102,40 @@ def setup_log(self, log_fn: str) -> None:
         sem.ErrorsToLog()
         sem.SetDirectory(os.getcwd())
 
-    def select_camera(self) -> None:
+    def select_camera(self, camera_num: Optional[int] = None) -> None:
         """ Choose camera to use. """
-
-        camera_num = 1
-        camera_names = []
-        while True:
-            name = sem.ReportCameraName(camera_num)
-            if name == "NOCAM":
-                break
-            else:
-                camera_names.append(name)
-                camera_num += 1
-
-        print("Choose camera to use with SerialEM:\n")
-        for i, c in enumerate(camera_names):
-            print(f"\t[{i + 1}] {c}")
-
-        camera_num = int(input("\nInput the camera number: ").strip())
-        if camera_num > len(camera_names) or camera_num < 1:
-            raise IndexError("Wrong camera number!")
-        else:
-            sem.SelectCamera(camera_num)
-            self.CAMERA_NUM = camera_num
-            cam_name = sem.ReportCameraName(self.CAMERA_NUM)
-            if "Falcon" in cam_name:
-                self.CAMERA_MODE = 0
-                self.CAMERA_HAS_DIVIDEBY2 = False
-            elif "K2" or "K3" in cam_name:
-                self.CAMERA_MODE = 1  # always counting
-                self.CAMERA_HAS_DIVIDEBY2 = True
-
-            _, _, mode = sem.ReportMag()
-            if mode == 1:  # EFTEM
-                sem.SetSlitIn(0)  # retract slit
+        if camera_num is None:  # enter from cmd, not GUI
+            camera_num = 1
+            camera_names = []
+            while True:
+                name = sem.ReportCameraName(camera_num)
+                if name == "NOCAM":
+                    break
+                else:
+                    camera_names.append(name)
+                    camera_num += 1
+
+            print("Choose camera to use with SerialEM:\n")
+            for i, c in enumerate(camera_names):
+                print(f"\t[{i + 1}] {c}")
+
+            camera_num = int(input("\nInput the camera number: ").strip())
+            if camera_num > len(camera_names) or camera_num < 1:
+                raise IndexError("Wrong camera number!")
+
+        sem.SelectCamera(camera_num)
+        self.CAMERA_NUM = camera_num
+        cam_name = sem.ReportCameraName(self.CAMERA_NUM)
+        if "K2" or "K3" in cam_name:
+            self.CAMERA_MODE = 1  # always counting
+            self.CAMERA_HAS_DIVIDEBY2 = True
+        if "Falcon 4" in cam_name:
+            self.CAMERA_MODE = 1  # always counting
+            self.CAMERA_HAS_DIVIDEBY2 = False
+
+        _, _, mode = sem.ReportMag()
+        if mode == 1:  # EFTEM
+            sem.SetSlitIn(0)  # retract slit
 
         if not sem.ReportColumnOrGunValve():
             print("Opening col. valves...")
@@ -170,6 +171,7 @@ def run(self) -> None:
         logging.info(f"Starting script {test_name} {start_time.strftime('%d/%m/%Y %H:%M:%S')}")
 
         try:
+            sem.SetImageShift(0, 0)
             if abs(sem.ReportTiltAngle()) > 0.1:
                 sem.TiltTo(0)
             self._run()
@@ -183,7 +185,6 @@ def run(self) -> None:
 
     def check_eps(self) -> None:
         """ Check max eps after setup beam but before area setup. """
-        # TODO: verify minimum dose rate for Falcon3/4
 
         logging.info("Checking dose rate...")
         old_exp, _ = sem.ReportExposure("F")
@@ -202,7 +203,7 @@ def check_eps(self) -> None:
                 spot += 1
 
         if spot != int(sem.ReportSpotSize()) and spot < 12:
-            logging.info(f"Increasing spot size to {spot} to reduce dose rate below 120 eps")
+            logging.info(f"Increasing spot size to {spot} to reduce dose rate below 200 eps")
             sem.SetSpotSize(spot)
 
         # Restore previous settings
@@ -258,7 +259,8 @@ def setup_beam(self, mag: int, spot: int, beamsize: float,
     def setup_area(self, exp: float, binning: int,
                    area: str = "F",
                    preset: str = "F",
-                   mode: Optional[str] = None) -> None:
+                   mode: Optional[int] = None,
+                   frames: Optional[bool] = False) -> None:
         """ Setup camera settings for a certain preset. """
 
         logging.info(f"Setting camera: preset={preset}, exp={exp}, binning={binning}, area={area}")
@@ -271,15 +273,19 @@ def setup_area(self, exp: float, binning: int,
         sem.NoMessageBoxOnError()
         try:
             sem.SetK2ReadMode(preset, camera_mode)  # linear=0, counting=1
-            sem.SetDoseFracParams(preset, 0, 0, 0)  # no frames
+            if frames:
+                sem.SetFrameTime(preset, 0.000001)  # will be fixed by SEM to a min number
+                sem.SetDoseFracParams(preset, 1, 0, 1, 1, 0)  # align frames with SEM plugin
+            else:
+                sem.SetDoseFracParams(preset, 0, 0, 0, 0, 0)  # no frames
         except sem.SEMerror or sem.SEMmoduleError:
             pass
         sem.NoMessageBoxOnError(0)
 
         logging.info("Setting camera: done!")
 
     @staticmethod
-    def euc_by_stage(fine: bool = False) -> None:
+    def euc_by_stage(fine: bool = True) -> None:
         """ Check FOV before running eucentricity by stage. """
         min_fov = sem.ReportProperty("EucentricityCoarseMinField")  # um
         pix = sem.ReportCurrentPixelSize("T")  # nm, with binning
@@ -290,9 +296,9 @@ def euc_by_stage(fine: bool = False) -> None:
                             f"{area} um < EucentricityCoarseMinField={min_fov}, "
                             "SerialEM will decrease the magnification automatically")
         sem.SetAbsoluteFocus(0)
-        sem.ChangeFocus(-50)
+        sem.ChangeFocus(-30)
         sem.Eucentricity(2 if fine else 1)
-        sem.ChangeFocus(50)
+        sem.ChangeFocus(30)
 
     def euc_by_beamtilt(self) -> None:
         """ Adapted from https://sphinx-emdocs.readthedocs.io/en/latest/serialEM-note-more-about-z-height.html#z-byv2-function """
@@ -351,7 +357,7 @@ def autofocus(target: float, precision: float = 0.05,
         logging.info(f"Autofocusing to {target} um...")
         sem.AutoFocus()
 
-        if high_mag:
+        if high_mag and target < -0.7:
             # fix astigmatism again, closer to focus
             sem.FixAstigmatismByCTF()