deapi 5.2.2__tar.gz → 5.3b0__tar.gz

{deapi-5.2.2 → deapi-5.3b0}/CHANGES.rst

@@ -5,8 +5,11 @@ Changelog
 
 This document describes the changes in the DEAPI library.
 
+5.3.beta0
+=========
+- Add support for binning in x/ y dimensions when returning a result (#19)
 
-Unreleased
+5.2.2
 ==========
 - Initial release
 - Renamed `Client` functions from CamelCase to snake_case (Legacy functions are still available)

{deapi-5.2.2 → deapi-5.3b0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deapi
-Version: 5.2.2
+Version: 5.3b0
 Summary: API for DE Server
 Author: Direct Electron
 Project-URL: Bug Reports, https://github.com/directelectron/deapi/issues

{deapi-5.2.2 → deapi-5.3b0}/deapi/client.py

@@ -193,8 +193,10 @@ class Client:
 
         version = [int(part) for part in server_version[:4]]
         temp = version[2] + version[1] * 1000 + version[0] * 1000000
-
-        if temp >= 2007004:
+        if temp >= 2007005:
+            ## version after 2.7.5
+            self.commandVersion = 15
+        elif temp >= 2007004:
             ## version after 2.7.4
             self.commandVersion = 13
         elif temp >= 2007003:
@@ -1410,37 +1412,48 @@ class Client:
             log.debug(" Prepare Time: %.1f ms", lapsed)
             step_time = self.GetTime()
 
-        histo_min = histogram.min
-        histo_max = histogram.max
-        histo_bins = histogram.bins
-
-        if self.width * self.height == 0:
-            log.error("  Image size is 0! ")
-        else:
-            bytesize = 0
-            command = self._addSingleCommand(
-                self.GET_RESULT,
-                None,
+        # Account for different command versions
+        params = [
+            frame_type.value,
+            pixel_format.value,
+            attributes.centerX,
+            attributes.centerY,
+            attributes.zoom,
+            attributes.windowWidth,
+            attributes.windowHeight,
+            attributes.fft,
+        ]
+        if commandVersion >= 10:
+            params.extend(
                 [
-                    frame_type.value,
-                    pixel_format.value,
-                    attributes.centerX,
-                    attributes.centerY,
-                    attributes.zoom,
-                    attributes.windowWidth,
-                    attributes.windowHeight,
-                    attributes.fft,
                     attributes.stretchType,
                     attributes.manualStretchMin,
                     attributes.manualStretchMax,
                     attributes.manualStretchGamma,
-                    attributes.outlierPercentage,
-                    attributes.timeoutMsec,
-                    histo_min,
-                    histo_max,
-                    histo_bins,
-                ],
+                ]
             )
+        else:
+            params.append(attributes.linearStretch)
+        params.append(attributes.outlierPercentage)
+        if commandVersion > 2 and commandVersion < 10:
+            params.append(attributes.buffered)
+        if commandVersion > 3:
+            params.append(attributes.timeoutMsec)
+        params.extend([histogram.min, histogram.max, histogram.bins])
+        if commandVersion >= 15:
+            params.extend(
+                [
+                    attributes.output_binning_x,
+                    attributes.output_binning_y,
+                    attributes.output_binning_method,
+                ]
+            )
+
+        if self.width * self.height == 0:
+            log.error("  Image size is 0! ")
+        else:
+            bytesize = 0
+            command = self._addSingleCommand(self.GET_RESULT, None, params=params)
 
             if logLevel == logging.DEBUG:
                 lapsed = (self.GetTime() - step_time) * 1000
@@ -2119,38 +2132,69 @@ class Client:
             print(" %.1fs" % duration)
             sys.stdout.flush()
 
-    # Start acquisition and get a single image
-    # fileName: the image will be saved to disk if a file name is provided
-    # textSize: a text file with pixel values will be saved if textSize is given, for debugging/test
-    def get_image(self, pixelFormat=PixelFormat.AUTO, fileName=None, textSize=0):
+    def _get_auto_attributes(self, frame_type: FrameType):
+        """
+        Get automatic attributes for the current acquisition settings.
+        Returns
+        -------
+        Attributes
+            The automatic attributes for the current acquisition settings.
+        """
+        attributes = Attributes()
+        scan_images = [17, 18, 19, 20, 21, 22, 23, 24, 25]
+        if frame_type.value in scan_images:
+            attributes.windowWidth = self.scan_sizex
+            attributes.windowHeight = self.scan_sizey
+        else:
+            attributes.windowWidth = self.image_sizex
+            attributes.windowHeight = self.image_sizey
+        return attributes
+
+    @deprecated_argument("pixelFormat", alternative="pixel_format", since="5.2.1")
+    @deprecated_argument("fileName", alternative="file_name", since="5.2.1")
+    @deprecated_argument("textSize", alternative="text_size", since="5.2.1")
+    def get_image(
+        self,
+        frame_type: Union[FrameType, str] = FrameType.SUMTOTAL,
+        pixel_format: Union[PixelFormat, str] = PixelFormat.AUTO,
+        attributes: Union[Attributes, str] = "auto",
+        file_name: str = None,
+        text_size: int = 0,
+    ):
         """
         Get a single image and save it to disk if a file name is provided
 
         Parameters
         ----------
-        pixelFormat : PixelFormat, optional
+        frame_type : FrameType or str, optional
+            The frame type of the image, by default FrameType.SUMTOTAL
+        pixel_format : PixelFormat, optional
             The pixel format of the image, by default PixelFormat.AUTO
-        fileName : str, optional
+        file_name : str, optional
             The file name to save the image, by default None
-        textSize : int, optional
+        attributes : Attributes or "auto", optional
+            The attributes of the image, by default "auto"
+        text_size : int, optional
             The text size, by default 0
         """
+        if isinstance(frame_type, str):
+            frame_type = getattr(FrameType, frame_type.upper())
+        if attributes == "auto":
+            attributes = self._get_auto_attributes(frame_type)
 
         self.StartAcquisition(1)
-        frameType = FrameType.SUMTOTAL
 
-        if pixelFormat == "float32":
-            pixelFormat = PixelFormat.FLOAT32
+        if pixel_format == "float32":
+            pixel_format = PixelFormat.FLOAT32
 
-        elif pixelFormat == "uint16":
-            pixelFormat = PixelFormat.UINT16
+        elif pixel_format == "uint16":
+            pixel_format = PixelFormat.UINT16
 
-        attributes = Attributes()
         histogram = Histogram()
-        image = self.GetResult(frameType, pixelFormat, attributes, histogram)[0]
+        image = self.GetResult(frame_type, pixel_format, attributes, histogram)[0]
 
-        if fileName and len(fileName) > 0:
-            self.SaveImage(image, fileName, textSize)
+        if file_name and len(file_name) > 0:
+            self.SaveImage(image, file_name, text_size)
 
         return image
 

{deapi-5.2.2 → deapi-5.3b0}/deapi/data_types.py

@@ -137,6 +137,13 @@ class ContrastStretchType(IntEnum):
     WIDERANGE = 7
 
 
+class BinningMethod(IntEnum):
+    NONE = 0
+    AVERAGE = 1
+    SUM = 2
+    FOURIERCROP = 3
+
+
 class Attributes:
     """Class to hold attributes for getting the result of an image acquisition
 
@@ -164,8 +171,79 @@ class Attributes:
         Maximum value for manual contrast stretching
     manual_stretch_gamma : float, optional
         Gamma value for manual contrast stretching
-
-
+    outlier_percentage : float, optional
+        Percentage of outliers to ignore in the image
+    buffered : bool, optional
+        Whether the image is buffered
+    timeout_msec : float, optional
+        Timeout in milliseconds for retrieving the image
+    frame_width : int, optional
+        Width of the frame in pixels
+    frame_height : int, optional
+        Height of the frame in pixels
+    dataset_name : str, optional
+        Name of the dataset to retrieve the image from
+    acq_index : int, optional
+        Index of the acquisition. Returned by the server with a get_result call.
+    acq_finished : bool, optional
+        Whether the acquisition is finished. Returned by the server with a get_result call.
+    image_index : int, optional
+        Index of the image in the acquisition. Returned by the server with a get_result call.
+    frame_count : int, optional
+        Number of frames in the acquisition. Returned by the server with a get_result call.
+    image_min : float, optional
+        Minimum value of the image data
+    image_max : float, optional
+        Maximum value of the image data
+    image_mean : float, optional
+        Mean value of the image data
+    image_std : float, optional
+        Standard deviation of the image data
+    eppix : float, optional
+        Electrons per pixel in the image
+    eps : float, optional
+        Electrons per second in the image
+    eppixps : float, optional
+        Electrons per pixel per second in the image
+    epa2 : float, optional
+        Electrons per area squared in the image
+    eppixpf : float, optional
+        Electrons per pixel per frame in the image
+    red_sat_warning_value : float, optional
+        Red saturation warning value for the image
+    orange_sat_warning_value : float, optional
+        Orange saturation warning value for the image
+    eppix_incident : float, optional
+        Electrons per pixel incident in the image
+    eps_incident : float, optional
+        Electrons per second incident in the image
+    eppixps_incident : float, optional
+        Electrons per pixel per second incident in the image
+    epa2_incident : float, optional
+        Electrons per area squared incident in the image
+    eppixpf_incident : float, optional
+        Electrons per pixel per frame incident in the image
+    under_exposure_rate : float, optional
+        Under exposure rate of the image
+    over_exposure_rate : float, optional
+        Over exposure rate of the image
+    timestamp : float, optional
+        Timestamp of the image acquisition
+    auto_stretch_min : float, optional
+        Minimum value for automatic contrast stretching
+    auto_stretch_max : float, optional
+        Maximum value for automatic contrast stretching
+    auto_stretch_gamma : float, optional
+        Gamma value for automatic contrast stretching
+    saturation : float, optional
+        Saturation level of the image
+    output_binning_x : int, optional
+        Binning factor in the x direction for the output image
+    output_binning_y : int, optional
+        Binning factor in the y direction for the output image
+    output_binning_method : int, optional
+        Method used for binning the output image. Defaults to BinningMethod.AVERAGE,
+        other options are BinningMethod.NONE, BinningMethod.SUM, and BinningMethod.FOURIERCROP.
     """
 
     def __init__(
@@ -214,6 +292,9 @@ class Attributes:
         auto_stretch_max=0.0,
         auto_stretch_gamma=1.0,
         saturation=0.0,
+        output_binning_x: int = 1,
+        output_binning_y: int = 1,
+        output_binning_method: int = 1,  # BinningMethod.AVERAGE
     ):
 
         self.centerX = center_x
@@ -260,6 +341,9 @@ class Attributes:
         self.autoStretchMax = auto_stretch_max
         self.autoStretchGamma = auto_stretch_gamma
         self.saturation = saturation
+        self.output_binning_x = output_binning_x
+        self.output_binning_y = output_binning_y
+        self.output_binning_method = output_binning_method
 
 
 class Histogram:

{deapi-5.2.2 → deapi-5.3b0}/deapi/prop_dump.json

@@ -384,7 +384,7 @@
         "get": "((hardware_roi_size_y / hardware_binning_y)/ binning_y)-crop_offset_y"
     },
   "Server Software Version":{
-    "value":"2.7.4.1352",
+    "value":"2.7.5.1352",
     "data_type":"String",
     "value_type":"ReadOnly",
     "category":"Basic",

{deapi-5.2.2 → deapi-5.3b0}/deapi/tests/test_fake_server/test_server.py

@@ -32,4 +32,4 @@ class TestFakeServer:
         assert fake_server["Scan - Virtual Detector 1 Calculation"] == "Sum"
 
     def test_server_software_version(self, fake_server):
-        assert fake_server["Server Software Version"] == "2.7.4.1352"
+        assert fake_server["Server Software Version"] == "2.7.5.1352"

deapi-5.3b0/deapi/version.py

@@ -0,0 +1,4 @@
+version = "5.3.0"
+versionInfo = list(map(int, version.split(".")))
+commandVersion = (versionInfo[0] - 4) * 10 + versionInfo[1] + 2
+print(f"DEAPI Version: {version} (Command Version: {commandVersion})")

{deapi-5.2.2 → deapi-5.3b0}/deapi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: deapi
-Version: 5.2.2
+Version: 5.3b0
 Summary: API for DE Server
 Author: Direct Electron
 Project-URL: Bug Reports, https://github.com/directelectron/deapi/issues

{deapi-5.2.2 → deapi-5.3b0}/pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "sympy",
 ]
 description = "API for DE Server"
-version = "5.2.2"
+version = "5.3b0"
 keywords = [
     "EELS",
     "STEM",

deapi-5.2.2/deapi/version.py

@@ -1,3 +0,0 @@
-version = "5.2.2"
-versionInfo = list(map(int, version.split(".")))
-commandVersion = (versionInfo[0] - 4) * 10 + versionInfo[1] + 1