waveorder 2.2.1__py3-none-any.whl → 3.0.0__py3-none-any.whl

waveorder/_version.py

@@ -1,7 +1,14 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -9,13 +16,19 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
 
-__version__ = version = '2.2.1'
-__version_tuple__ = version_tuple = (2, 2, 1)
+__version__ = version = '3.0.0'
+__version_tuple__ = version_tuple = (3, 0, 0)
+
+__commit_id__ = commit_id = None

waveorder/acq/acq_functions.py

@@ -0,0 +1,166 @@
+import glob
+import json
+import os
+import time
+
+import numpy as np
+from iohub.mmstack import MMStack
+
+try:
+    from pycromanager import Studio
+except:
+    pass
+
+
+def generate_acq_settings(
+    mm,
+    channel_group,
+    channels=None,
+    zstart=None,
+    zend=None,
+    zstep=None,
+    save_dir=None,
+    prefix=None,
+    keep_shutter_open_channels=False,
+    keep_shutter_open_slices=False,
+):
+    """
+    This function generates a json file specific to the Micro-Manager SequenceSettings.
+    It has default parameters for a multi-channels z-stack acquisition but does not yet
+    support multi-position or multi-frame acquisitions.
+
+    This also has default values for QLIPP Acquisition.  Can be used as a framework for other types
+    of acquisitions
+
+    Parameters
+    ----------
+    mm:             (object) MM Studio API object
+    scheme:         (str) '4-State' or '5-State'
+    zstart:         (float) relative starting position for the z-stack
+    zend:           (float) relative ending position for the z-stack
+    zstep:          (float) step size for the z-stack
+    save_dir:       (str) path to save directory
+    prefix:         (str) name to save the data under
+
+    Returns
+    -------
+    settings:       (json) json dictionary conforming to MM SequenceSettings
+    """
+
+    # Get API Objects
+    am = mm.getAcquisitionManager()
+    ss = am.getAcquisitionSettings()
+    app = mm.app()
+
+    # Get current SequenceSettings to modify
+    original_ss = ss.toJSONStream(ss)
+    original_json = json.loads(original_ss).copy()
+
+    if zstart:
+        do_z = True
+    else:
+        do_z = False
+
+    # Structure of the channel properties
+    channel_dict = {
+        "channelGroup": channel_group,
+        "config": None,
+        "exposure": None,
+        "zOffset": 0,
+        "doZStack": do_z,
+        "color": {"value": -16747854, "falpha": 0.0},
+        "skipFactorFrame": 0,
+        "useChannel": True if channels else False,
+    }
+
+    channel_list = None
+    if channels:
+        # Append all the channels with their current exposure settings
+        channel_list = []
+        for chan in channels:
+            # todo: think about how to deal with missing exposure
+            exposure = app.getChannelExposureTime(
+                channel_group, chan, 10
+            )  # sets exposure to 10 if not found
+            channel = channel_dict.copy()
+            channel["config"] = chan
+            channel["exposure"] = exposure
+
+            channel_list.append(channel)
+
+    # set other parameters
+    original_json["numFrames"] = 1
+    original_json["intervalMs"] = 0
+    original_json["relativeZSlice"] = True
+    original_json["slicesFirst"] = True
+    original_json["timeFirst"] = False
+    original_json["keepShutterOpenSlices"] = keep_shutter_open_slices
+    original_json["keepShutterOpenChannels"] = keep_shutter_open_channels
+    original_json["useAutofocus"] = False
+    original_json["saveMode"] = "MULTIPAGE_TIFF"
+    original_json["save"] = True if save_dir else False
+    original_json["root"] = save_dir if save_dir else ""
+    original_json["prefix"] = prefix if prefix else "Untitled"
+    original_json["channels"] = channel_list
+    original_json["zReference"] = 0.0
+    original_json["channelGroup"] = channel_group
+    original_json["usePositionList"] = False
+    original_json["shouldDisplayImages"] = True
+    original_json["useSlices"] = do_z
+    original_json["useFrames"] = False
+    original_json["useChannels"] = True if channels else False
+    original_json["slices"] = (
+        list(np.arange(float(zstart), float(zend + zstep), float(zstep)))
+        if zstart
+        else []
+    )
+    original_json["sliceZStepUm"] = zstep
+    original_json["sliceZBottomUm"] = zstart
+    original_json["sliceZTopUm"] = zend
+    original_json["acqOrderMode"] = 1
+
+    return original_json
+
+
+def acquire_from_settings(
+    mm: Studio,
+    settings: dict,
+    grab_images: bool = True,
+    restore_settings: bool = True,
+) -> np.typing.NDArray:
+    """Function to acquire an MDA acquisition with the native MM MDA Engine.
+    Assumes single position acquisition.
+
+    Parameters
+    ----------
+    mm : Studio
+    settings : dict
+        JSON dictionary conforming to MM SequenceSettings
+    grab_images : bool, optional
+        return the acquired array, by default True
+    restore_settings : bool, optional
+        restore MDA settings before acquisition, by default True
+
+    Returns
+    -------
+    NDArray
+        acquired images
+    """
+    am = mm.getAcquisitionManager()
+    ss = am.getAcquisitionSettings()
+
+    ss_new = ss.fromJSONStream(json.dumps(settings))
+    am.runAcquisitionWithSettings(ss_new, True)
+
+    time.sleep(3)
+
+    if restore_settings:
+        am.setAcquisitionSettings(ss)
+
+    # TODO: speed improvements in reading the data with pycromanager acquisition?
+    if grab_images:
+        # get the most recent acquisition if multiple
+        path = os.path.join(settings["root"], settings["prefix"])
+        files = glob.glob(path + "*")
+        index = max([int(x.split(path + "_")[1]) for x in files])
+        return MMStack(path + f"_{index}")[0].xdata.to_numpy()