pymmcore-plus 0.10.2__py3-none-any.whl → 0.11.0__py3-none-any.whl

pymmcore_plus/model/_microscope.py

@@ -15,6 +15,7 @@ from ._pixel_size_config import PixelSizeGroup
 
 if TYPE_CHECKING:
     from pymmcore_plus import CMMCorePlus
+    from pymmcore_plus.metadata.schema import SummaryMetaV1
 
     from ._core_link import ErrCallback
     from ._property import Property
@@ -126,7 +127,7 @@ class Microscope:
     # ------------- Config-file methods -------------
 
     @classmethod
-    def create_from_config(cls, config_file: str) -> Microscope:
+    def create_from_config(cls, config_file: str | Path) -> Microscope:
         obj = cls()
         obj.load_config(config_file)
         obj.mark_clean()
@@ -154,6 +155,39 @@ class Microscope:
 
         self.mark_clean()
 
+    @classmethod
+    def from_summary_metadata(cls, summary_meta: SummaryMetaV1) -> Microscope:
+        """Create a Microscope model from summary metadata.
+
+        This may be used to load a model from summary metadata, such as as written
+        during the course of a Multi-Dimensional Acquisition.  This is useful for
+        restoring the state of a microscope from a specific experiment, or writing
+        out a cfg file that can be used to restore the state of the microscope.
+        """
+        core_device = next(
+            (d for d in summary_meta["devices"] if d["name"] == Keyword.CoreDevice),
+            None,
+        )
+        if core_device is None:
+            raise ValueError("CoreDevice not found in metadata")
+        return cls(
+            core_device=CoreDevice.from_metadata(core_device),
+            devices=[
+                Device.from_metadata(d)
+                for d in summary_meta["devices"]
+                if d["name"] != Keyword.CoreDevice
+            ],
+            config_groups={
+                grp["name"]: ConfigGroup.from_metadata(grp)
+                for grp in summary_meta["config_groups"]
+            },
+            pixel_size_group=PixelSizeGroup.from_metadata(
+                summary_meta["pixel_size_configs"]
+            ),
+            config_file=summary_meta["system_info"].get("system_configuration_file")
+            or "",
+        )
+
     # ------------- Core-interacting methods -------------
 
     @classmethod

pymmcore_plus/model/_pixel_size_config.py

@@ -1,16 +1,20 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field, fields
-from typing import TYPE_CHECKING, Any, Container, Iterable, MutableMapping
+from typing import TYPE_CHECKING
 
 from ._config_group import ConfigGroup, ConfigPreset, Setting
 
 if TYPE_CHECKING:
-    from typing import Final
+    from typing import Any, Container, Final, Iterable, MutableMapping
 
-    from typing_extensions import TypeAlias  # py310
+    from typing_extensions import (
+        Self,  # py311
+        TypeAlias,  # py310
+    )
 
     from pymmcore_plus import CMMCorePlus
+    from pymmcore_plus.metadata.schema import PixelSizeConfigPreset
 
     from ._core_link import ErrCallback
 
@@ -27,6 +31,14 @@ class PixelSizePreset(ConfigPreset):
     pixel_size_um: float = 0.0
     affine: AffineTuple = DEFAULT_AFFINE
 
+    @classmethod
+    def from_metadata(cls, meta: PixelSizeConfigPreset) -> Self:  # type: ignore [override]
+        obj = super().from_metadata(meta)
+        obj.pixel_size_um = meta["pixel_size_um"]
+        if "pixel_size_affine" in meta:
+            obj.affine = meta["pixel_size_affine"]
+        return obj
+
     def __rich_repr__(self, *, defaults: bool = False) -> Iterable[tuple[str, Any]]:
         """Make AvailableDevices look a little less verbose."""
         for f in fields(self):
@@ -45,6 +57,16 @@ class PixelSizeGroup(ConfigGroup):
     name: str = PIXEL_SIZE_GROUP
     presets: MutableMapping[str, PixelSizePreset] = field(default_factory=dict)  # type: ignore
 
+    @classmethod
+    def from_metadata(cls, meta: tuple[PixelSizeConfigPreset, ...]) -> Self:  # type: ignore [override]
+        """Create a PixelSizeGroup from metadata."""
+        return cls(
+            presets={
+                preset_info["name"]: PixelSizePreset.from_metadata(preset_info)
+                for preset_info in meta
+            }
+        )
+
     @classmethod
     def create_from_core(
         cls, core: CMMCorePlus, name: str = PIXEL_SIZE_GROUP

{pymmcore_plus-0.10.2.dist-info → pymmcore_plus-0.11.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pymmcore-plus
-Version: 0.10.2
+Version: 0.11.0
 Summary: pymmcore superset providing improved APIs, event handling, and a pure python acquisition engine
 Project-URL: Source, https://github.com/pymmcore-plus/pymmcore-plus
 Project-URL: Tracker, https://github.com/pymmcore-plus/pymmcore-plus/issues
@@ -47,6 +47,7 @@ Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: tensorstore-stubs; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocs-typer==0.0.3; extra == 'docs'
 Requires-Dist: mkdocs>=1.4; extra == 'docs'
 Requires-Dist: mkdocstrings-python==1.1.2; extra == 'docs'
 Requires-Dist: mkdocstrings==0.22.0; extra == 'docs'
@@ -55,6 +56,7 @@ Requires-Dist: tifffile>=2021.6.14; extra == 'io'
 Requires-Dist: zarr>=2.2; extra == 'io'
 Provides-Extra: test
 Requires-Dist: msgpack; extra == 'test'
+Requires-Dist: msgspec; extra == 'test'
 Requires-Dist: pytest-cov>=4; extra == 'test'
 Requires-Dist: pytest-qt>=4; extra == 'test'
 Requires-Dist: pytest>=7.3.2; extra == 'test'
@@ -143,8 +145,7 @@ provides a python API to control the C++ core directly, without the need for
 Java in the loop.  Each has its own advantages and disadvantages!  With
 pycro-manager you immediately get the entire existing micro-manager ecosystem
 and GUI application. With pymmcore-plus you don't need to install Java, and you
-have direct access to the memory buffers used by the C++ core, but the GUI
-side of things is far less mature.
+have direct access to the memory buffers used by the C++ core.
 
 ## Quickstart
 

pymmcore_plus-0.11.0.dist-info/RECORD

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+pymmcore_plus-0.11.0.dist-info/licenses/LICENSE,sha256=OHJjRpOPKKRc7FEnpehNWdR5LRBdBhUtIFG-ZI0dCEA,1522
+pymmcore_plus-0.11.0.dist-info/RECORD,,

{pymmcore_plus-0.10.2.dist-info → pymmcore_plus-0.11.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.24.2
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pymmcore_plus/core/_state.py

@@ -1,244 +0,0 @@
-from __future__ import annotations
-
-from contextlib import suppress
-from typing import TYPE_CHECKING, Any, Literal, Sequence, TypedDict, cast
-
-if TYPE_CHECKING:
-    from pymmcore_plus import CMMCorePlus
-
-
-class SystemInfoDict(TypedDict):
-    APIVersionInfo: str
-    BufferFreeCapacity: int
-    BufferTotalCapacity: int
-    CircularBufferMemoryFootprint: int
-    DeviceAdapterSearchPaths: tuple[str, ...]
-    PrimaryLogFile: str
-    RemainingImageCount: int
-    TimeoutMs: int  # rarely needed for metadata
-    VersionInfo: str
-    # these were removed in mmcore11 and probably shouldn't be used anyway
-    # HostName: str
-    # MACAddresses: tuple[str, ...]
-    # UserId: str
-
-
-class ImageDict(TypedDict):
-    BytesPerPixel: int
-    CurrentPixelSizeConfig: str
-    Exposure: float
-    ImageBitDepth: int
-    ImageBufferSize: int
-    ImageHeight: int
-    ImageWidth: int
-    MagnificationFactor: float
-    MultiROI: tuple[list[int], list[int], list[int], list[int]] | None
-    NumberOfCameraChannels: int
-    NumberOfComponents: int
-    PixelSizeAffine: tuple[float, float, float, float, float, float]
-    PixelSizeUm: int
-    ROI: list[int]
-
-
-class PositionDict(TypedDict):
-    X: float | None
-    Y: float | None
-    Focus: float | None
-
-
-class AutoFocusDict(TypedDict):
-    CurrentFocusScore: float
-    LastFocusScore: float
-    AutoFocusOffset: float | None
-
-
-class PixelSizeConfigDict(TypedDict):
-    Objective: dict[str, str]
-    PixelSizeUm: float
-    PixelSizeAffine: tuple[float, float, float, float, float, float]
-
-
-class DeviceTypeDict(TypedDict):
-    Type: str
-    Description: str
-    Adapter: str
-
-
-class SystemStatusDict(TypedDict):
-    debugLogEnabled: bool
-    isBufferOverflowed: bool
-    isContinuousFocusEnabled: bool
-    isContinuousFocusLocked: bool
-    isSequenceRunning: bool
-    stderrLogEnabled: bool
-    systemBusy: bool
-    autoShutter: bool
-    shutterOpen: bool
-
-
-class StateDict(TypedDict, total=False):
-    Devices: dict[str, dict[str, str]]
-    SystemInfo: SystemInfoDict
-    SystemStatus: SystemStatusDict
-    ConfigGroups: dict[str, dict[str, Any]]
-    Image: ImageDict
-    Position: PositionDict
-    AutoFocus: AutoFocusDict
-    PixelSizeConfig: dict[str, str | PixelSizeConfigDict]
-    DeviceTypes: dict[str, DeviceTypeDict]
-
-
-def core_state(
-    core: CMMCorePlus,
-    *,
-    devices: bool = True,
-    image: bool = True,
-    system_info: bool = False,
-    system_status: bool = False,
-    config_groups: bool | Sequence[str] = True,
-    position: bool = False,
-    autofocus: bool = False,
-    pixel_size_configs: bool = False,
-    device_types: bool = False,
-    cached: bool = True,
-    error_value: Any = None,
-) -> StateDict:
-    out: StateDict = {}
-    if devices:
-        out["Devices"] = get_device_state(core, error_value)
-    if system_info:
-        out["SystemInfo"] = get_system_info(core)
-    if system_status:
-        out["SystemStatus"] = get_system_status(core)
-    if config_groups:
-        out["ConfigGroups"] = get_config_groups(core, config_groups, cached)
-    if image:
-        out["Image"] = get_image_info(core, error_value)
-    if position:
-        out["Position"] = get_position(core, error_value)
-    if autofocus:
-        out["AutoFocus"] = get_autofocus(core, error_value)
-    if pixel_size_configs:
-        out["PixelSizeConfig"] = get_pix_size_config(core)
-    if device_types:
-        out["DeviceTypes"] = get_device_types(core)
-    return out
-
-
-def get_device_state(
-    core: CMMCorePlus, cached: bool = True, error_value: Any = None
-) -> dict[str, dict[str, Any]]:
-    # this actually appears to be faster than getSystemStateCache
-    getProp = core.getPropertyFromCache if cached else core.getProperty
-    device_state: dict = {}
-    for dev in core.getLoadedDevices():
-        dd = device_state.setdefault(dev, {})
-        for prop in core.getDevicePropertyNames(dev):
-            try:
-                val = getProp(dev, prop)
-            except Exception:
-                val = error_value
-            dd[prop] = val
-    return device_state
-
-
-def get_system_info(core: CMMCorePlus) -> SystemInfoDict:
-    return {  # type: ignore
-        key: getattr(core, f"get{key}")()
-        for key in sorted(SystemInfoDict.__annotations__)
-    }
-
-
-def get_system_status(core: CMMCorePlus) -> SystemStatusDict:
-    out = {
-        "autoShutter": core.getAutoShutter(),
-        "shutterOpen": core.getShutterOpen(),
-    }
-    out.update(
-        {
-            key: getattr(core, key)()
-            for key in sorted(SystemStatusDict.__annotations__)
-            if key not in {"autoShutter", "shutterOpen"}
-        }
-    )
-    return cast("SystemStatusDict", out)
-
-
-def get_config_groups(
-    core: CMMCorePlus,
-    config_groups: bool | Sequence[str | Literal["[Channel]"]],
-    cached: bool = True,
-) -> dict[str, dict[str, Any]]:
-    if not isinstance(config_groups, (list, tuple, set)):
-        config_groups = core.getAvailableConfigGroups()
-
-    getState = core.getConfigGroupStateFromCache if cached else core.getConfigGroupState
-    curGrp = core.getCurrentConfigFromCache if cached else core.getCurrentConfig
-    cfg_group_dict: dict = {}
-    for grp in config_groups:
-        if grp == "[Channel]":
-            # special case for accessing channel group
-            grp = core.getChannelGroup()
-
-        grp_dict = cfg_group_dict.setdefault(grp, {})
-        grp_dict["Current"] = curGrp(grp)
-
-        for dev, prop, val in getState(grp):
-            grp_dict.setdefault(dev, {})[prop] = val
-    return cfg_group_dict
-
-
-def get_image_info(core: CMMCorePlus, error_value: Any = None) -> ImageDict:
-    img_dict = {}
-    for key in sorted(ImageDict.__annotations__):
-        try:
-            val = getattr(core, f"get{key}")()
-        except Exception:
-            val = error_value
-        img_dict[key] = val
-    return cast("ImageDict", img_dict)
-
-
-def get_position(core: CMMCorePlus, error_value: Any = None) -> PositionDict:
-    pos: PositionDict = {"X": error_value, "Y": error_value, "Focus": error_value}
-    with suppress(Exception):
-        pos["X"] = core.getXPosition()
-        pos["Y"] = core.getYPosition()
-    with suppress(Exception):
-        pos["Focus"] = core.getPosition()
-    return pos
-
-
-def get_autofocus(core: CMMCorePlus, error_value: Any = None) -> AutoFocusDict:
-    out: AutoFocusDict = {
-        "CurrentFocusScore": core.getCurrentFocusScore(),
-        "LastFocusScore": core.getLastFocusScore(),
-        "AutoFocusOffset": error_value,
-    }
-    with suppress(Exception):
-        out["AutoFocusOffset"] = core.getAutoFocusOffset()
-    return out
-
-
-def get_pix_size_config(core: CMMCorePlus) -> dict[str, str | PixelSizeConfigDict]:
-    # the Current value is a string, all the rest are PixelSizeConfigDict
-    px: dict = {"Current": core.getCurrentPixelSizeConfig()}
-    for px_cfg_name in core.getAvailablePixelSizeConfigs():
-        px_cfg_info: dict = {}
-        for dev, prop, val in core.getPixelSizeConfigData(px_cfg_name):
-            px_cfg_info.setdefault(dev, {})[prop] = val
-        px_cfg_info["PixelSizeUm"] = core.getPixelSizeUmByID(px_cfg_name)
-        px_cfg_info["PixelSizeAffine"] = core.getPixelSizeAffineByID(px_cfg_name)
-        px[px_cfg_name] = px_cfg_info
-    return px
-
-
-def get_device_types(core: CMMCorePlus) -> dict[str, DeviceTypeDict]:
-    return {
-        dev_name: {
-            "Type": core.getDeviceType(dev_name).name,
-            "Description": core.getDeviceDescription(dev_name),
-            "Adapter": core.getDeviceName(dev_name),
-        }
-        for dev_name in core.getLoadedDevices()
-    }

pymmcore_plus-0.10.2.dist-info/RECORD

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