modacor 1.0.0__py3-none-any.whl

modacor/tests/io/tiled/test_tiled_source.py

@@ -0,0 +1,120 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+__coding__ = "utf-8"
+__authors__ = ["Brian R. Pauw"]  # add names to the list as appropriate
+__copyright__ = "Copyright 2026, The MoDaCor team"
+__date__ = "20/01/2026"
+__status__ = "Development"  # "Development", "Production"
+# end of header and standard imports
+
+import numpy as np
+import pytest
+
+from modacor.io.tiled.tiled_source import TiledSource
+
+
+class _DummyStructure:
+    def __init__(self, shape, dtype):
+        self.shape = tuple(shape)
+        self.dtype = dtype
+
+
+class _DummyLeaf:
+    def __init__(self, data: np.ndarray, metadata: dict[str, object] | None = None):
+        self._data = np.asarray(data)
+        self.metadata = metadata or {}
+
+    def read(self, slice=None):
+        if slice is None:
+            return self._data
+        return self._data[slice]
+
+    @property
+    def shape(self):
+        return self._data.shape
+
+    @property
+    def dtype(self):
+        return self._data.dtype
+
+    def structure(self):
+        return _DummyStructure(self._data.shape, self._data.dtype)
+
+    @property
+    def attrs(self):
+        return self.metadata.get("attrs", {})
+
+
+class _DummyNode:
+    def __init__(self, children: dict[str, object], metadata: dict[str, object] | None = None):
+        self._children = children
+        self.metadata = metadata or {}
+
+    def __getitem__(self, item: str):
+        return self._children[item]
+
+    @property
+    def attrs(self):
+        return self.metadata.get("attrs", {})
+
+
+@pytest.fixture
+def dummy_source() -> TiledSource:
+    root = _DummyNode(
+        {
+            "entry": _DummyNode(
+                {
+                    "data": _DummyLeaf(
+                        data=np.arange(6).reshape(2, 3),
+                        metadata={"attrs": {"units": "counts"}},
+                    ),
+                    "scalar": _DummyLeaf(np.array(42)),
+                },
+                metadata={"attrs": {"title": "Example"}},
+            )
+        }
+    )
+
+    return TiledSource(
+        source_reference="dummy",
+        root_node=root,
+        iosource_method_kwargs={"base_item_path": "entry"},
+    )
+
+
+def test_tiled_source_reads_array(dummy_source: TiledSource):
+    data = dummy_source.get_data("data")
+    np.testing.assert_array_equal(data, np.arange(6).reshape(2, 3))
+
+    cached = dummy_source.get_data("data")
+    np.testing.assert_array_equal(cached, data)
+
+
+def test_tiled_source_slicing(dummy_source: TiledSource):
+    sliced = dummy_source.get_data("data", load_slice=np.s_[1, :])
+    np.testing.assert_array_equal(sliced, np.array([3, 4, 5]))
+
+
+def test_tiled_source_shape_dtype(dummy_source: TiledSource):
+    assert dummy_source.get_data_shape("data") == (2, 3)
+    assert dummy_source.get_data_dtype("data") == np.dtype(int)
+
+
+def test_tiled_source_attributes(dummy_source: TiledSource):
+    attrs = dummy_source.get_data_attributes("data")
+    assert attrs == {"units": "counts"}
+
+    assert dummy_source.get_static_metadata("data@units") == "counts"
+    # For metadata without explicit attribute name, the full metadata mapping is returned
+    metadata = dummy_source.get_static_metadata("data")
+    assert metadata == {"attrs": {"units": "counts"}}
+
+
+def test_tiled_source_resolves_base_metadata(dummy_source: TiledSource):
+    assert dummy_source.get_static_metadata("") == {}
+    assert dummy_source.get_static_metadata("scalar") == {}
+    np.testing.assert_array_equal(dummy_source.get_data("scalar"), np.array(42))

modacor/tests/io/yaml/__init__.py

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+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright 2025 MoDaCor Authors
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 3. Neither the name of the copyright holder nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+__license__ = "BSD-3-Clause"
+__copyright__ = "Copyright 2025 MoDaCor Authors"
+__status__ = "Alpha"

modacor/tests/io/yaml/static_data_example.yaml

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+--- # Datafile with examples of static metadata for MoDaCor's static IoSource
+instrument:
+  name: "MOUSE"
+  type: "X-ray scattering"
+  manufacturer: "In-house modified Xenocs"
+  model: "Xeuss 2.0"
+  serial_number: "1"
+probe_properties:
+  wavelength:
+    value: 0.1542
+    unit: "nm"
+    uncertainty: 0.0002
+geometry:
+  sample_position:
+    x:
+      value: 0.0
+      unit: "m"
+      uncertainty: 0.000
+    y:
+      value: 0.0
+      unit: "m"
+      uncertainty: 0.000
+    z:
+      value: 0.0
+      unit: "m"
+      uncertainty: 0.000

modacor/tests/io/yaml/test_yaml_source.py

@@ -0,0 +1,47 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+__coding__ = "utf-8"
+__authors__ = ["Brian R. Pauw"]
+__copyright__ = "Copyright 2025, The MoDaCor team"
+__date__ = "06/06/2025"
+__status__ = "Development"  # "Development", "Production"
+# end of header and standard imports
+
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+from ....io.yaml.yaml_source import YAMLSource
+
+filepath = Path(__file__).parent / "static_data_example.yaml"
+
+
+def test_yaml_source_initialization():
+    """
+    Test the initialization of the YAMLSource class.
+    """
+    source = YAMLSource(source_reference="defaults", resource_location=filepath)
+    source._preload()
+    assert isinstance(source._yaml_data, dict)
+    assert isinstance(source._data_cache, dict)
+
+
+def test_yaml_source_get_value():
+    source = YAMLSource(source_reference="defaults", resource_location=filepath)
+    source._preload()
+    # at this point, data_cache should be empty:
+    assert source._data_cache == {}
+    v = source.get_data("probe_properties/wavelength/value")
+    assert isinstance(v, np.ndarray)
+    # and now we should have the value in the cache:
+    assert "probe_properties/wavelength/value" in source._data_cache
+    # this should raise a valueerror as the string cannot be converted to a float array:
+    with pytest.raises(ValueError):
+        source.get_data("probe_properties/wavelength/unit")
+    # but this works:
+    assert source.get_static_metadata("probe_properties/wavelength/unit") == "nm"

modacor/tests/modules/__init__.py

@@ -0,0 +1,27 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright 2025 MoDaCor Authors
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 3. Neither the name of the copyright holder nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+__license__ = "BSD-3-Clause"
+__copyright__ = "Copyright 2025 MoDaCor Authors"
+__status__ = "Alpha"

modacor/tests/modules/base_modules/__init__.py

@@ -0,0 +1,27 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright 2025 MoDaCor Authors
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+# 3. Neither the name of the copyright holder nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+__license__ = "BSD-3-Clause"
+__copyright__ = "Copyright 2025 MoDaCor Authors"
+__status__ = "Alpha"

modacor/tests/modules/base_modules/test_append_processing_data.py

@@ -0,0 +1,219 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+__coding__ = "utf-8"
+__authors__ = ["Brian R. Pauw"]  # add names to the list as appropriate
+__copyright__ = "Copyright 2025, The MoDaCor team"
+__date__ = "03/12/2025"
+__status__ = "Development"  # "Development", "Production"
+# end of header and standard imports
+
+from typing import Any
+
+import numpy as np
+import pytest
+from attrs import define, field
+
+from modacor import ureg
+from modacor.dataclasses.basedata import BaseData
+from modacor.dataclasses.databundle import DataBundle
+from modacor.dataclasses.processing_data import ProcessingData
+from modacor.io.io_source import IoSource
+from modacor.io.io_sources import IoSources
+from modacor.modules.base_modules.append_processing_data import AppendProcessingData
+
+
+@define(kw_only=True)
+class MemoryIoSource(IoSource):
+    """
+    Minimal in-memory IoSource for tests.
+
+    - `data_key` is the part AFTER '<source_ref>::' (IoSources does that split).
+    - get_data supports slicing via numpy indexing.
+    - get_static_metadata returns whatever was stored.
+    """
+
+    data: dict[str, np.ndarray] = field(factory=dict)
+    metadata: dict[str, Any] = field(factory=dict)
+
+    def get_data(self, data_key: str, load_slice=...) -> np.ndarray:
+        arr = self.data[data_key]
+        return arr[load_slice]
+
+    def get_data_shape(self, data_key: str) -> tuple[int, ...]:
+        return tuple(self.data[data_key].shape) if data_key in self.data else ()
+
+    def get_data_dtype(self, data_key: str):
+        return self.data[data_key].dtype if data_key in self.data else None
+
+    def get_data_attributes(self, data_key: str) -> dict[str, Any]:
+        # Not needed in these tests
+        return {}
+
+    def get_static_metadata(self, data_key: str) -> Any:
+        return self.metadata[data_key]
+
+
+@pytest.fixture
+def signal_array():
+    return np.arange(6, dtype=float).reshape(2, 3)
+
+
+@pytest.fixture
+def io_sources(signal_array) -> IoSources:
+    """
+    Build a real IoSources with one registered MemoryIoSource under source_ref='sample'.
+    """
+    sources = IoSources()
+
+    src = MemoryIoSource(
+        source_reference="sample",
+        data={
+            "entry/instrument/detector/data": signal_array,
+            "entry/instrument/detector/sigma": np.ones_like(signal_array),
+        },
+        metadata={
+            "config/rank": 1,
+            "entry/instrument/detector/data@units": "dimensionless",
+        },
+    )
+
+    sources.register_source(src)
+    return sources
+
+
+def _make_step(io_sources: IoSources, processing_data: ProcessingData | None = None) -> AppendProcessingData:
+    if processing_data is None:
+        processing_data = ProcessingData()
+    step = AppendProcessingData(io_sources=io_sources, processing_data=processing_data)
+    return step
+
+
+# --------------------------------------------------------------------------- #
+# 1. Basic creation: new DataBundle with default output key "signal"
+# --------------------------------------------------------------------------- #
+def test_append_processing_data_creates_new_bundle(io_sources, signal_array):
+    step = _make_step(io_sources)
+
+    step.modify_config_by_dict(
+        {
+            "processing_key": "sample",
+            "signal_location": "sample::entry/instrument/detector/data",
+            "rank_of_data": 2,
+            "units_location": None,
+            "units_override": None,
+            "uncertainties_sources": {},
+        }
+    )
+
+    output = step.calculate()
+
+    assert list(output.keys()) == ["sample"]
+    bundle = output["sample"]
+    assert isinstance(bundle, DataBundle)
+
+    assert "sample" in step.processing_data
+    assert step.processing_data["sample"] is bundle
+
+    assert "signal" in bundle
+    bd = bundle["signal"]
+    assert isinstance(bd, BaseData)
+    np.testing.assert_array_equal(bd.signal, signal_array)
+
+    assert bd.units == ureg.dimensionless
+    assert bd.rank_of_data == 2
+    assert bundle.default_plot == "signal"
+
+
+# --------------------------------------------------------------------------- #
+# 2. Updating an existing DataBundle (reusing processing_key)
+# --------------------------------------------------------------------------- #
+def test_append_processing_data_updates_existing_bundle(io_sources, signal_array):
+    processing_data = ProcessingData()
+
+    existing_bundle = DataBundle()
+    existing_bd = BaseData(signal=np.ones_like(signal_array), units=ureg.dimensionless)
+    existing_bundle["existing"] = existing_bd
+    existing_bundle.default_plot = "existing"
+    processing_data["sample"] = existing_bundle
+
+    step = _make_step(io_sources, processing_data=processing_data)
+
+    step.modify_config_by_dict(
+        {
+            "processing_key": "sample",
+            "signal_location": "sample::entry/instrument/detector/data",
+            "rank_of_data": 1,
+            "databundle_output_key": "I",
+            "units_location": None,
+            "units_override": None,
+            "uncertainties_sources": {},
+        }
+    )
+
+    output = step.calculate()
+
+    assert list(output.keys()) == ["sample"]
+    bundle = output["sample"]
+    assert bundle is existing_bundle
+
+    assert "existing" in bundle
+    assert bundle["existing"] is existing_bd
+
+    assert "I" in bundle
+    bd_I = bundle["I"]
+    np.testing.assert_array_equal(bd_I.signal, signal_array)
+    assert bd_I.rank_of_data == 1
+
+    assert bundle.default_plot == "existing"
+
+
+# --------------------------------------------------------------------------- #
+# 3. rank_of_data resolved from IoSources metadata (string reference)
+# --------------------------------------------------------------------------- #
+def test_append_processing_data_rank_from_metadata(io_sources):
+    step = _make_step(io_sources)
+
+    step.modify_config_by_dict(
+        {
+            "processing_key": "sample",
+            "signal_location": "sample::entry/instrument/detector/data",
+            "rank_of_data": "sample::config/rank",
+            "units_location": None,
+            "units_override": None,
+            "uncertainties_sources": {},
+        }
+    )
+
+    output = step.calculate()
+    bd = output["sample"]["signal"]
+    assert bd.rank_of_data == 1
+
+
+# --------------------------------------------------------------------------- #
+# 4. uncertainties_sources wiring
+# --------------------------------------------------------------------------- #
+def test_append_processing_data_adds_uncertainties(io_sources, signal_array):
+    step = _make_step(io_sources)
+
+    step.modify_config_by_dict(
+        {
+            "processing_key": "sample",
+            "signal_location": "sample::entry/instrument/detector/data",
+            "rank_of_data": 2,
+            "units_location": None,
+            "units_override": None,
+            "uncertainties_sources": {
+                "sigma": "sample::entry/instrument/detector/sigma",
+            },
+        }
+    )
+
+    output = step.calculate()
+    bd = output["sample"]["signal"]
+
+    assert "sigma" in bd.uncertainties
+    np.testing.assert_array_equal(bd.uncertainties["sigma"], np.ones_like(signal_array))

modacor/tests/modules/base_modules/test_append_sink.py

@@ -0,0 +1,76 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+__coding__ = "utf-8"
+__authors__ = ["Brian R. Pauw"]
+__copyright__ = "Copyright 2026, The MoDaCor team"
+__date__ = "09/01/2026"
+__status__ = "Development"  # "Development", "Production"
+# end of header and standard imports
+
+from pathlib import Path
+
+import pytest
+
+from modacor.io.csv.csv_sink import CSVSink
+from modacor.io.io_sinks import IoSinks
+from modacor.modules.base_modules.append_sink import AppendSink
+
+
+@pytest.fixture
+def io_sinks():
+    return IoSinks()
+
+
+def _make_step(io_sinks: IoSinks) -> AppendSink:
+    step = AppendSink()
+    step.io_sinks = io_sinks
+    return step
+
+
+def test_append_sink_registers_csvsink(tmp_path: Path, io_sinks: IoSinks):
+    out_file = tmp_path / "export.csv"
+
+    step = _make_step(io_sinks)
+    step.modify_config_by_dict(
+        {
+            "sink_identifier": ["export_csv"],
+            "sink_location": [str(out_file)],
+            "iosink_module": "modacor.io.csv.csv_sink.CSVSink",
+            "iosink_method_kwargs": {"delimiter": ","},
+        }
+    )
+
+    output = step.calculate()
+    assert output == {}
+
+    assert "export_csv" in io_sinks.defined_sinks
+    sink = io_sinks.defined_sinks["export_csv"]
+    assert isinstance(sink, CSVSink)
+    assert sink.resource_location == out_file
+
+
+def test_append_sink_does_not_overwrite_existing_sink(tmp_path: Path, io_sinks: IoSinks):
+    out_file = tmp_path / "export.csv"
+
+    step = _make_step(io_sinks)
+    step.modify_config_by_dict(
+        {
+            "sink_identifier": ["export_csv"],
+            "sink_location": [str(out_file)],
+            "iosink_module": "modacor.io.csv.csv_sink.CSVSink",
+            "iosink_method_kwargs": {"delimiter": ","},
+        }
+    )
+
+    step.calculate()
+    first = io_sinks.defined_sinks["export_csv"]
+
+    # Run again: AppendSink should skip registering if id already exists
+    step.calculate()
+    second = io_sinks.defined_sinks["export_csv"]
+
+    assert first is second