v0.2.2 Release (#156)

### Highlights - OpenFIBSEM is now available on PyPI. Use pip to install: `pip install fibsem`. On ThermoFisher systems, OpenFIBSEM will automatically find your Autoscript installation if it installed. On Tescan, please install into the same environment as the Automation API. - Minimap: Added a minimap widget for collecting tiled images, selecting positions and correlation. Provides an overview of the current stage position and the positions of the selected locations. Also provides an integrated correlation user interface. You can use the minimap to select locations for other applications, such as AutoLamella. ### Features - Added a _safe_absolute_stage_movement. This function will tilt flat before performing large movements to prevent collions. - Added cleaning_cross_section and scan_direction to the milling widget user interface. - Rectangle Patterns now sputter a 'passes' parameter. This allows you to explicitly set the number of passes the beam will scan. - Adjusted the milling widget to allow for the selection of multiple milling stages. This allows you to move multiple stages together. - Added automatic logging for alignment data. All alignment data is now logged to a file in the log/crosscorrelation directory. You can change this log directory in the config. - Added a cryo sputter widget for automated sputtering in cryo conditions. - Added two way projection between image and stage coordinates. This allows you to click on an image and move the stage to that location, as well as project a stage coordinate to an image coordinate (currently located in fibsem.imaging._tile). - To move milling stages in the UI, you now need to 'Shift' + 'Left Click' (Was 'Right Click') - To move the stage vertically (eucentric_move), you now need to 'Alt' + 'Left Click' (Was previously an option in the UI). ### Fixes / Updates - Fixed an issue where masks were not calculated for alignment.correct_stage_drift. - Changed the model checkpoint lookup to search the fibsem/segmentation/models directory instead of expecting an absolute path. - Fixed an issue where coordinate system was flipped when moving using a detection. - Fixed an issue where milling protocols were being overwritten when setting the milling stages directly. [USER-INTERFACE] - The milling widget hfw should now update automatically when changing the imaging settings. [USER-INTERFACE] - The user interface won't try to draw the cross hair if no image is available. [USER-INTERFACE] - Explicitly converting the last_image to np.uint8 (was np.uint16) [THERMO] - Explictly settings the manipulator coordinate system when performing movements [THERMO] - Post milling current now set to 30keV: 150 pA instead of 30keV: UHR Imaging [TESCAN] - Fixed milling rate conversions, where the milling rate units were not converted correctly [TESCAN]
DeMarcoLab · Aug 2, 2023 · ba7ea68 · ba7ea68
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -5,7 +5,7 @@ on:
       - v0.2-stable
   pull_request:
     branches:
-      - v0.2-stable
+      - v0.2-release
 jobs:
   deploy:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -5,7 +5,7 @@ name: Python package
 
 on:
   pull_request:
-    branches: [ "v0.2-stable" ]
+    branches: [ "v0.2-release" ]
 
 jobs:
   build:

diff --git a/.gitignore b/.gitignore
@@ -49,3 +49,7 @@ fibsem/segmentation/models/*
 example/**/*.tif
 example/demo/*
 fibsem/chat/secret.txt
+
+dist/*
+scratch/tile-images/*
+fibsem/log/*
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,6 +1,38 @@
-## Changes
+# Changes
 
-### 12/07/2023
+## v0.2.2 - 31/07/2023
+
+### Highlights
+
+- OpenFIBSEM is now available on PyPI. Use pip to install: `pip install fibsem`. On ThermoFisher systems, OpenFIBSEM will automatically find your Autoscript installation if it installed. On Tescan, please install into the same environment as the Automation API.
+- Minimap: Added a minimap widget for collecting tiled images, selecting positions and correlation. Provides an overview of the current stage position and the positions of the selected locations. Also provides an integrated correlation user interface. You can use the minimap to select locations for other applications, such as AutoLamella.  
+
+### Features
+
+- Added a _safe_absolute_stage_movement. This function will tilt flat before performing large movements to prevent collions.
+- Added cleaning_cross_section and scan_direction to the milling widget user interface.
+- Rectangle Patterns now sputter a 'passes' parameter. This allows you to explicitly set the number of passes the beam will scan.
+- Adjusted the milling widget to allow for the selection of multiple milling stages. This allows you to move multiple stages together.
+- Added automatic logging for alignment data. All alignment data is now logged to a file in the log/crosscorrelation directory. You can change this log directory in the config.
+- Added a cryo sputter widget for automated sputtering in cryo conditions.
+- Added two way projection between image and stage coordinates. This allows you to click on an image and move the stage to that location, as well as project a stage coordinate to an image coordinate (currently located in fibsem.imaging._tile).
+- To move milling stages in the UI, you now need to 'Shift' + 'Left Click' (Was 'Right Click')
+- To move the stage vertically (eucentric_move), you now need to 'Alt' + 'Left Click' (Was previously an option in the UI).
+
+### Fixes / Updates
+
+- Fixed an issue where masks were not calculated for alignment.correct_stage_drift.
+- Changed the model checkpoint lookup to search the fibsem/segmentation/models directory instead of expecting an absolute path.
+- Fixed an issue where coordinate system was flipped when moving using a detection.
+- Fixed an issue where milling protocols were being overwritten when setting the milling stages directly. [USER-INTERFACE]
+- The milling widget hfw should now update automatically when changing the imaging settings. [USER-INTERFACE]
+- The user interface won't try to draw the cross hair if no image is available. [USER-INTERFACE]
+- Explicitly converting the last_image to np.uint8 (was np.uint16) [THERMO]
+- Explictly settings the manipulator coordinate system when performing movements [THERMO]
+- Post milling current now set to 30keV: 150 pA instead of 30keV: UHR Imaging [TESCAN]
+- Fixed milling rate conversions, where the milling rate units were not converted correctly [TESCAN]
+
+## 12/07/2023
 
 - Added Documentation
       - Added documentation for the detection and labelling widget
@@ -14,12 +46,12 @@
       - Added a fibsem version number for development tracking
       - Live chat (experimental)
       - Autoliftout utils
-      - GIS Widget for cryo-control of gas injection 
+      - GIS Widget for cryo-control of gas injection
       - Embedded detection widget
 
 - Fixed bugs
       - fixed issue where parameters were passed incorrectly for milling
-      - fixed Eucentric movement where z-direction was flipped 
+      - fixed Eucentric movement where z-direction was flipped
 
 - Updated Functionality / Improved Processes
       - system/model yaml files can now be modified from the system widget
@@ -28,26 +60,23 @@
       - An option to click to move multiple milling stages together is now available
       - Added a crosshair to the images
       - movement of milling pattern now emits a pyqt signal (backend)
-      - Manufacturer / model /serial no info can now be accessed/saved 
-      - Manipulator UI adaptive based on if manipulator is retracted or inserted 
-      - Enabled granular hardware control for stage and manipulator (backend), eg: disable rotation only 
-
+      - Manufacturer / model /serial no info can now be accessed/saved
+      - Manipulator UI adaptive based on if manipulator is retracted or inserted
+      - Enabled granular hardware control for stage and manipulator (backend), eg: disable rotation only
 
-### 24/05/2023
+## 24/05/2023
 
 - Added new features
       - FIB current alignment
       - Manipulator Controls
       - Measurement tools
       - Segment Anything Labelling
       - Added new milling patterns (Bitmap, Annulus)
-      - Separated stage pretilt 
+      - Separated stage pretilt
 - Fixed bugs
       - Autolamella example
       - Set microscope stage
-      - HFW 
+      - HFW
       - Milling widget
       - Application file/Presets set on startup
-      - Import TESCAN image files 
-
-
+      - Import TESCAN image files
diff --git a/fibsem/acquire.py b/fibsem/acquire.py
@@ -38,10 +38,14 @@ def take_reference_images(
         - The `FibsemImage` objects in the returned tuple contain the image data as numpy arrays,
           as well as other image metadata.
     """
+    import time 
+    from fibsem.microscope import TescanMicroscope
     tmp_beam_type = image_settings.beam_type
     image_settings.beam_type = BeamType.ELECTRON
     eb_image = new_image(microscope, image_settings)
     image_settings.beam_type = BeamType.ION
+    if isinstance(microscope, TescanMicroscope):
+        time.sleep(3)
     ib_image = new_image(microscope, image_settings)
     image_settings.beam_type = tmp_beam_type  # reset to original beam type
 
@@ -88,6 +92,15 @@ def take_set_of_reference_images(
 
     reference_images = ReferenceImages(low_eb, high_eb, low_ib, high_ib)
 
+
+    # more flexible version
+    # reference_images = []
+    # for i, hfw in enumerate(hfws):
+    #     image_settings.hfw = hfw
+    #     image_settings.label = f"{label}_res_{i:02d}"
+    #     eb_image, ib_image = take_reference_images(microscope, image_settings)
+    #     reference_images.append([eb_image, ib_image])
+
     return reference_images
 
 

diff --git a/fibsem/alignment.py b/fibsem/alignment.py
@@ -16,7 +16,7 @@
     FibsemRectangle,
 )
 from fibsem.microscope import FibsemMicroscope
-from typing import Union
+from typing import Union, Optional
 
 
 def auto_eucentric_correction(
@@ -51,7 +51,7 @@ def beam_shift_alignment(
     microscope: FibsemMicroscope,
     image_settings: ImageSettings,
     ref_image: FibsemImage,
-    reduced_area: FibsemRectangle = None,
+    reduced_area: Optional[FibsemRectangle] = None,
 ):
     """Aligns the images by adjusting the beam shift instead of moving the stage.
 
@@ -71,6 +71,8 @@ def beam_shift_alignment(
         ValueError: If `image_settings.beam_type` is not set to `BeamType.ION`.
 
     """
+    image_settings = ImageSettings.fromFibsemImage(ref_image)
+    image_settings.beam_type = BeamType.ION
     image_settings.reduced_area = reduced_area
     new_image = acquire.new_image(
         microscope, settings=image_settings
@@ -89,10 +91,10 @@ def correct_stage_drift(
     reference_images: ReferenceImages,
     alignment: tuple[BeamType, BeamType] = (BeamType.ELECTRON, BeamType.ELECTRON),
     rotate: bool = False,
-    use_ref_mask: bool = False,
-    mask_scale: int = 4,
+    ref_mask_rad: int = 512,
     xcorr_limit: Union[tuple[int, int], None] = None,
     constrain_vertical: bool = False,
+    use_beam_shift: bool = False,
 ) -> bool:
     """Corrects the stage drift by aligning low- and high-resolution reference images
     using cross-correlation.
@@ -108,10 +110,7 @@ def correct_stage_drift(
             BeamType.ELECTRON).
         rotate (bool, optional): Whether to rotate the reference images before
             alignment. Defaults to False.
-        use_ref_mask (bool, optional): Whether to apply a mask to the reference images
-            before alignment. Defaults to False.
-        mask_scale (int, optional): The scale factor used for creating the mask. Defaults
-            to 4.
+        ref_mask_rad (int, optional): The radius of the circular mask used for reference
         xcorr_limit (tuple[int, int] | None, optional): A tuple of two integers that
             represent the minimum and maximum cross-correlation values allowed for the
             alignment. If not specified, the values are set to (None, None), which means
@@ -146,21 +145,10 @@ def correct_stage_drift(
     # align lowres, then highres
     for i, ref_image in enumerate([ref_lowres, ref_highres]):
 
-        if use_ref_mask:
-            ref_mask = masks.create_lamella_mask(
-                ref_image,
-                settings.protocol["lamella"],
-                scale=mask_scale,
-                use_trench_height=True,
-            )  # TODO: refactor, liftout specific
-        else:
-            ref_mask = None
+        ref_mask = masks.create_circle_mask(ref_image.data.shape, ref_mask_rad)
 
         # take new images
         # set new image settings (same as reference)
-        # settings.image = utils.match_image_settings(
-        #     ref_image, settings.image, beam_type=alignment[1]
-        # )
         settings.image = ImageSettings.fromFibsemImage(ref_image)
         settings.image.beam_type = alignment[1]
         new_image = acquire.new_image(microscope, settings.image)
@@ -174,6 +162,7 @@ def correct_stage_drift(
             ref_mask=ref_mask,
             xcorr_limit=xcorr_limit[i],
             constrain_vertical=constrain_vertical,
+            use_beam_shift=use_beam_shift,
         )
 
         if ret is False:
@@ -190,6 +179,7 @@ def align_using_reference_images(
     ref_mask: np.ndarray = None,
     xcorr_limit: int = None,
     constrain_vertical: bool = False,
+    use_beam_shift: bool = False,
 ) -> bool:
     """
     Uses cross-correlation to align a new image to a reference image.
@@ -245,13 +235,17 @@ def align_using_reference_images(
                 settings=settings, dy=-dy
             )  # FLAG_TEST
         else:
-            # move the stage
-            microscope.stable_move(
-                settings=settings,
-                dx=dx,
-                dy=-dy,
-                beam_type=new_beam_type,
-            )
+            if use_beam_shift:
+                # move the beam shift
+                microscope.beam_shift(dx=-dx, dy=dy, beam_type=new_beam_type)
+            else:
+                # move the stage
+                microscope.stable_move(
+                    settings=settings,
+                    dx=dx,
+                    dy=-dy,
+                    beam_type=new_beam_type,
+                )
 
     return shift_within_tolerance
 
@@ -326,17 +320,35 @@ def shift_from_crosscorrelation(
     err = np.array(cen - [maxX, maxY], int)
 
     # calculate shift in metres
-    x_shift = err[1] * pixelsize_x
-    y_shift = err[0] * pixelsize_y  # this could be the issue?
+    dx = err[1] * pixelsize_x
+    dy = err[0] * pixelsize_y  # this could be the issue?
 
     logging.debug(f"cross-correlation:")
     logging.debug(f"pixelsize: x: {pixelsize_x:.2e}, y: {pixelsize_y:.2e}")
     logging.debug(f"maxX: {maxX}, {maxY}, centre: {cen}")
     logging.debug(f"x: {err[1]}px, y: {err[0]}px")
-    logging.debug(f"x: {x_shift:.2e}m, y: {y_shift:.2e} meters")
+    logging.debug(f"x: {dx:.2e}m, y: {dy:.2e} meters")
+
+    # save data
+    _save_alignment_data(
+        ref_image=ref_image,
+        new_image=new_image,
+        bandpass=bandpass,
+        xcorr=xcorr,
+        use_rect_mask=use_rect_mask,
+        ref_mask=ref_mask,
+        xcorr_limit=xcorr_limit,
+        lowpass=lowpass,
+        highpass=highpass,
+        sigma=sigma,
+        dx=dx,
+        dy=dy,
+        pixelsize_x=pixelsize_x,
+        pixelsize_y=pixelsize_y,
+    )
 
     # metres
-    return x_shift, y_shift, xcorr
+    return dx, dy, xcorr
 
 
 def crosscorrelation_v2(
@@ -388,3 +400,59 @@ def crosscorrelation_v2(
     xcorr = np.real(np.fft.fftshift(np.fft.ifft2(img1ft * np.conj(img2ft))))
 
     return xcorr
+
+def _save_alignment_data(
+    ref_image: FibsemImage,
+    new_image: FibsemImage,
+    bandpass: np.ndarray,
+    xcorr: np.ndarray,
+    ref_mask: np.ndarray = None,
+    lowpass: float = None,
+    highpass: float = None,
+    sigma: float = None,
+    xcorr_limit: float = None,
+    use_rect_mask: bool = False,
+    dx: float = None,
+    dy: float = None,
+    pixelsize_x: float = None,
+    pixelsize_y: float = None,
+
+
+):
+    """Save alignment data to disk."""
+
+    import pandas as pd
+    import os
+    from fibsem import config as cfg
+    import tifffile as tff
+
+    ts = utils.current_timestamp_v2()
+    fname = os.path.join(cfg.DATA_CC_PATH, str(ts))
+
+    # save fibsem images
+    ref_image.save(fname + "_ref.tif")
+    new_image.save(fname + "_new.tif")
+
+    # convert to tiff , save
+    tff.imwrite(fname + "_xcorr.tif", xcorr)
+    tff.imwrite(fname + "_bandpass.tif", bandpass)
+    if ref_mask is not None:
+        tff.imwrite(fname + "_ref_mask.tif", ref_mask)
+
+    info = {
+        # "ref_image": ref_image, "new_image": new_image, "bandpass": bandpass, "xcorr": xcorr, "ref_mask": ref_mask,
+        "lowpass": lowpass, "highpass": highpass, "sigma": sigma,
+        "pixelsize_x": pixelsize_x, "pixelsize_y": pixelsize_y, 
+        "use_rect_mask": use_rect_mask, "xcorr_limit": xcorr_limit, "ref_mask": ref_mask is not None,
+        "dx": dx, "dy": dy, "fname": fname, "timestamp": ts }
+
+
+    df = pd.DataFrame.from_dict(info, orient='index').T
+
+    # save the dataframe to a csv file, append if the file already exists
+    DATAFRAME_PATH = os.path.join(cfg.DATA_CC_PATH, "data.csv")
+    if os.path.exists(DATAFRAME_PATH):
+        df_tmp = pd.read_csv(DATAFRAME_PATH)
+        df = pd.concat([df_tmp, df], axis=0, ignore_index=True)
+
+    df.to_csv(DATAFRAME_PATH, index=False)
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,7 +5,7 @@ name: Python package @@
     on:
       pull_request:
-        branches: [ "v0.2-stable" ]
+        branches: [ "v0.2-release" ]
     jobs:
       build:
@@ Expand Down @@