mirror of
https://github.com/slsdetectorgroup/aare.git
synced 2026-10-28 19:21:27 +01:00
Erik Fröjdh
7abbf3cbb5
Third part of splitting up dev/gap. The multithreaded reader comes in the next PR. - `RawFile` takes an optional `GapPixels`. Frames are assembled with the gaps inserted: fill the gap lines, scatter each module part through the scratch buffer into its gapped position, and split the chip edge counts if configured. `rows()`, `cols()`, `pixels_per_frame()` and `bytes_per_frame()` include the gaps, for the full frame and for each ROI. Only Jungfrau and Eiger are supported. - Python `RawFile` accepts `gap_pixels` as a bool or a `GapPixels`, exposes it as a property, and takes frame shapes from `rows()` and `cols()`. - The generic `File` is unchanged: it does not know the detector geometry of `.npy` and `.dat` files, so gap pixels stay a `RawFile` option. Use `RawFile`, or apply `insert_gap_pixels` to frames from `File`. - Tests: generalized raw file helper with arbitrary module layouts, module layout assembly tests (these cover #421, which went in without tests), synthetic gap tests, a split-counts oracle against `insert_gap_pixels`, unsupported detector rejection, and data-backed recorded-file and two-ROI cases. - A raw file benchmark with no-gaps, fill-value and split-counts cases. - Docs and release note.
614 lines
23 KiB
Python
614 lines
23 KiB
Python
# SPDX-License-Identifier: MPL-2.0
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import pytest
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import json
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from aare import File, RawFile, RawSubFile, DetectorType, ROI, UDPPortPosition, xy
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from aare import GapPixels, ModuleGaps, insert_gap_pixels
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import numpy as np
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@pytest.fixture
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def small_raw_file(tmp_path):
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master_path = tmp_path / "run_master_0.json"
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master_path.write_text(json.dumps({
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"Version": 7.2,
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"Detector Type": "Jungfrau",
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"Timing Mode": "auto",
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"Geometry": {"x": 1, "y": 1},
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"Image Size in bytes": 12,
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"Pixels": {"x": 3, "y": 2},
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"Max Frames Per File": 1,
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"Total Frames": 2,
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"Frames in File": 2,
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"Frame Padding": 1,
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"Frame Discard Policy": "nodiscard",
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}))
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for index in range(2):
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data_path = tmp_path / f"run_d0_f{index}_0.raw"
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# A detector header followed by six uint16 pixels.
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data_path.write_bytes(bytes(112) + np.arange(6, dtype=np.uint16).tobytes())
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return master_path
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MODULE_ROWS = 2
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MODULE_COLS = 3
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def write_module_layout(directory, layout_rows, layout_cols, frames=2,
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module_rows=MODULE_ROWS, module_cols=MODULE_COLS,
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detector_type="Jungfrau"):
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"""Write a raw file series with modules in the given layout.
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Modules are numbered as DetectorGeometry orders them, down each column
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first, and every module holds distinct values so misplacement is visible.
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Returns the master path and the expected image of frame 0.
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"""
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master_path = directory / "run_master_0.json"
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master_path.write_text(json.dumps({
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"Version": 7.2,
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"Detector Type": detector_type,
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"Timing Mode": "auto",
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"Geometry": {"x": layout_cols, "y": layout_rows},
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"Image Size in bytes": module_rows * module_cols * 2,
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"Pixels": {"x": module_cols, "y": module_rows},
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"Max Frames Per File": 1,
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"Total Frames": frames,
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"Frames in File": frames,
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"Frame Padding": 1,
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"Frame Discard Policy": "nodiscard",
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}))
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expected = np.zeros((module_rows * layout_rows, module_cols * layout_cols), dtype=np.uint16)
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for module in range(layout_rows * layout_cols):
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module_row, module_col = module % layout_rows, module // layout_rows
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pixels = ((np.arange(module_rows * module_cols, dtype=np.uint32) + module * 10 + 1) % 65536).astype(np.uint16)
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expected[module_row * module_rows:(module_row + 1) * module_rows,
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module_col * module_cols:(module_col + 1) * module_cols] = pixels.reshape(module_rows, module_cols)
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for index in range(frames):
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data_path = directory / f"run_d{module}_f{index}_0.raw"
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# 112 byte detector header followed by the module pixels
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data_path.write_bytes(bytes(112) + pixels.tobytes())
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return master_path, expected
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@pytest.mark.parametrize("reader_type", [RawFile, File])
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@pytest.mark.parametrize("legacy_master", [False, True])
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@pytest.mark.parametrize("padding, policy, supported", [
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(0, "nodiscard", False),
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(0, "discard", False),
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(0, "discardpartial", True),
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(1, "nodiscard", True),
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(1, "discard", True),
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(1, "discardpartial", True),
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])
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def test_raw_frame_policy(small_raw_file, reader_type, legacy_master,
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padding, policy, supported):
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master_path = small_raw_file
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if legacy_master:
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master_path = master_path.with_suffix(".raw")
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master_path.write_text(
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"Version : 6.4\n"
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"Detector Type : Jungfrau\n"
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"Timing Mode : auto\n"
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"Geometry : [1, 1]\n"
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"Image Size : 12\n"
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"Pixels : [3, 2]\n"
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"Dynamic Range : 16\n"
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"Max Frames Per File : 1\n"
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"Total Frames : 2\n"
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"Frames in File : 2\n"
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f"Frame Padding : {padding}\n"
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f"Frame Discard Policy : {policy}\n"
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)
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else:
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metadata = json.loads(master_path.read_text())
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metadata["Frame Padding"] = padding
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metadata["Frame Discard Policy"] = policy
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master_path.write_text(json.dumps(metadata))
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if supported:
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reader = reader_type(master_path)
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assert reader.total_frames == 2
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frame = reader.read_frame()
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if reader_type is RawFile:
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_, frame = frame
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np.testing.assert_array_equal(frame, np.arange(6).reshape(2, 3))
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else:
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message = "requires frame padding or discardpartial"
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with pytest.raises(RuntimeError, match=message) as error:
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reader_type(master_path)
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assert str(master_path) in str(error.value)
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for index in range(2):
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(master_path.parent / f"run_d0_f{index}_0.raw").unlink()
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with pytest.raises(RuntimeError, match=message) as error:
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reader_type(master_path)
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assert str(master_path) in str(error.value)
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@pytest.mark.parametrize("method, args, kwargs", [
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("read_frame", (), {}),
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("read_n", (1,), {}),
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("read_roi", (0,), {}),
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("read_rois", (), {}),
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("read_n_with_roi", (1,), {"roi_index": 0}),
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("frame_number", (2,), {}),
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])
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def test_raw_read_error_context(small_raw_file, method, args, kwargs):
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reader = RawFile(small_raw_file)
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reader.seek(2)
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with pytest.raises(RuntimeError) as error:
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getattr(reader, method)(*args, **kwargs)
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assert "frame index 2" in str(error.value)
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assert str(small_raw_file) in str(error.value)
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assert ".raw" not in str(error.value)
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if method == "read_frame":
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assert "file contains 2 frames (indices are zero-based)" in str(error.value)
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@pytest.mark.parametrize("frame_index", [2, 17])
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def test_generic_raw_read_error_context(small_raw_file, frame_index):
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reader = File(small_raw_file)
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with pytest.raises(RuntimeError) as error:
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reader.read_frame(frame_index)
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assert f"frame index {frame_index}" in str(error.value)
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assert str(small_raw_file) in str(error.value)
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@pytest.mark.parametrize("raw_subfile", [False, True])
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def test_truncated_raw_read_error_context(small_raw_file, raw_subfile):
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data_path = small_raw_file.parent / "run_d0_f1_0.raw"
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if raw_subfile:
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reader = RawSubFile(
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small_raw_file.parent / "run_d0_f0_0.raw",
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DetectorType.Jungfrau, 2, 3, 16,
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)
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else:
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reader = RawFile(small_raw_file)
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data_path.write_bytes(bytes(112))
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reader.seek(1)
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with pytest.raises(RuntimeError) as error:
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reader.read_frame()
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assert "frame index 1" in str(error.value)
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assert str(data_path) in str(error.value)
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assert "End of file" in str(error.value)
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assert "master" not in str(error.value)
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assert "RawSubFile.cpp" not in str(error.value)
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@pytest.mark.parametrize("method, args", [
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("read_frame", ()),
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("read_n", (1,)),
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("read_roi", (0,)),
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("frame_number", (1,)),
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])
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def test_short_raw_subfile_sets_read_bounds(small_raw_file, method, args):
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(small_raw_file.parent / "run_d0_f1_0.raw").unlink()
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reader = RawFile(small_raw_file)
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reader.seek(1)
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with pytest.raises(RuntimeError) as error:
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getattr(reader, method)(*args)
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assert reader.total_frames == 1
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assert "frame index 1" in str(error.value)
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assert str(small_raw_file) in str(error.value)
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assert ".raw" not in str(error.value)
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@pytest.mark.parametrize("counts, master_count, warn", [
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([2], 2, False),
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([2, 2], 2, False),
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([2, 2], 0, True),
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([2, 2], 1, True),
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([2, 2], 5, True),
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([1, 2], 2, True),
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([2, 1], 2, True),
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([1, 2], 1, True),
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([0, 2], 2, True),
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([0, 0], 0, False),
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])
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def test_raw_subfile_frame_counts(small_raw_file, capfd, counts, master_count, warn):
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metadata = json.loads(small_raw_file.read_text())
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metadata["Geometry"]["y"] = len(counts)
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metadata["Frames in File"] = master_count
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metadata["Total Frames"] = 1000
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small_raw_file.write_text(json.dumps(metadata))
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data = (small_raw_file.parent / "run_d0_f0_0.raw").read_bytes()
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for module, count in enumerate(counts):
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for index in range(2):
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path = small_raw_file.parent / f"run_d{module}_f{index}_0.raw"
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if index < count:
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path.write_bytes(data)
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elif index == 0:
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path.write_bytes(b"")
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else:
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path.unlink(missing_ok=True)
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reader = RawFile(small_raw_file)
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warning = capfd.readouterr().err
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if warn:
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assert warning.count("WARNING") == 1
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assert str(small_raw_file) in warning
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else:
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assert "WARNING" not in warning
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assert reader.total_frames == min(counts)
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assert len(reader) == min(counts)
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assert reader.master.frames_in_file == master_count
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if min(counts):
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_, frames = reader.read()
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assert frames.shape == (min(counts), 2 * len(counts), 3)
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reader.seek(0)
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_, frames = reader.read_n(10)
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assert len(frames) == min(counts)
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assert reader.frame_number(min(counts) - 1) == 0
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with pytest.raises(RuntimeError):
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reader.frame_number(min(counts))
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reader.seek(min(counts))
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with pytest.raises(RuntimeError):
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reader.read_frame()
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assert "WARNING" not in capfd.readouterr().err
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@pytest.mark.parametrize("short_module", [0, 1])
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def test_raw_frame_count_across_rois(small_raw_file, short_module):
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metadata = json.loads(small_raw_file.read_text())
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metadata.update({
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"Version": 8.0,
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"Geometry": {"x": 1, "y": 2},
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"Image Size": 12,
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"Receiver Rois": [
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{"xmin": 0, "xmax": 2, "ymin": 0, "ymax": 1},
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{"xmin": 0, "xmax": 2, "ymin": 2, "ymax": 3},
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],
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})
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small_raw_file.write_text(json.dumps(metadata))
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for index in range(2):
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data = (small_raw_file.parent / f"run_d0_f{index}_0.raw").read_bytes()
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(small_raw_file.parent / f"run_d1_f{index}_0.raw").write_bytes(data)
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(small_raw_file.parent / f"run_d{short_module}_f1_0.raw").unlink()
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reader = RawFile(small_raw_file)
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assert reader.total_frames == 1
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_, rois = reader.read_rois()
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assert len(rois) == 2
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assert all(roi.shape == (2, 3) for roi in rois)
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for roi_index in range(2):
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reader.seek(0)
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_, frames = reader.read_n_with_roi(10, roi_index=roi_index)
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assert frames.shape == (1, 2, 3)
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with pytest.raises(RuntimeError):
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reader.read_roi(roi_index)
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def test_raw_file_geometry(small_raw_file):
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metadata = json.loads(small_raw_file.read_text())
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metadata["Geometry"] = {"x": 1, "y": 2}
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small_raw_file.write_text(json.dumps(metadata))
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for index in range(2):
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data = (small_raw_file.parent / f"run_d0_f{index}_0.raw").read_bytes()
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(small_raw_file.parent / f"run_d1_f{index}_0.raw").write_bytes(data)
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reader = RawFile(small_raw_file)
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assert reader.geometry == xy(row=2, col=1)
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assert reader.master.detector_layout == xy(row=2, col=1)
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assert reader.master.udp_interfaces_per_module == xy(row=1, col=1)
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@pytest.mark.parametrize("disabled_port", [0, 1])
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def test_raw_frame_count_with_disabled_udp_port(small_raw_file, disabled_port):
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metadata = json.loads(small_raw_file.read_text())
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metadata.update({
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"Geometry": {"x": 1, "y": 2},
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"Frames in File": 0,
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"Number of UDP Interfaces": 2,
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"UDP Ports Type": ["bottom", "top"],
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"UDP Ports Disabled": [disabled_port],
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})
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small_raw_file.write_text(json.dumps(metadata))
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data = (small_raw_file.parent / "run_d0_f0_0.raw").read_bytes()
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for index in range(2):
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(small_raw_file.parent / f"run_d0_f{index}_0.raw").unlink()
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path = small_raw_file.parent / f"run_d{1 - disabled_port}_f{index}_0.raw"
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path.write_bytes(data)
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reader = RawFile(small_raw_file)
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assert reader.total_frames == 2
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assert reader.master.frames_in_file == 0
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assert reader.frame_number(1) == 0
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_, frames = reader.read()
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assert frames.shape == (2, 2, 3)
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def test_raw_frame_count_without_selected_subfiles(small_raw_file):
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metadata = json.loads(small_raw_file.read_text())
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metadata.update({"Version": 8.0, "Image Size": 12, "Receiver Rois": []})
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small_raw_file.write_text(json.dumps(metadata))
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with pytest.raises(RuntimeError, match="No raw subfiles selected"):
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RawFile(small_raw_file)
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@pytest.mark.parametrize("lagging_module", [0, 1])
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def test_raw_synchronization_error_identifies_subfile(
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small_raw_file, lagging_module
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):
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metadata = json.loads(small_raw_file.read_text())
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metadata["Geometry"]["y"] = 2
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small_raw_file.write_text(json.dumps(metadata))
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for index in range(2):
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data = (small_raw_file.parent / f"run_d0_f{index}_0.raw").read_bytes()
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(small_raw_file.parent / f"run_d1_f{index}_0.raw").write_bytes(data)
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ahead_path = small_raw_file.parent / f"run_d{1 - lagging_module}_f1_0.raw"
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with ahead_path.open("r+b") as output:
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output.write(np.array([1], dtype=np.uint64).tobytes())
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reader = RawFile(small_raw_file)
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reader.seek(1)
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with pytest.raises(RuntimeError) as error:
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reader.read_frame()
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assert "frame index 1" in str(error.value)
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assert "synchroniz" in str(error.value)
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lagging_path = small_raw_file.parent / f"run_d{lagging_module}_f1_0.raw"
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assert str(lagging_path) in str(error.value)
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@pytest.mark.withdata
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def test_read_rawfile_with_roi_spanning_over_one_module(test_data_path):
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with RawFile(test_data_path / "raw/ROITestData/SingleChipROI/Data_master_0.json") as f:
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headers, frames = f.read()
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num_rois = f.num_rois
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assert num_rois == 1
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assert headers.size == 10100
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assert frames.shape == (10100, 256, 256)
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assert headers.size == 10100
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assert frames.shape == (10100, 256, 256)
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@pytest.mark.withdata
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def test_read_rawfile_with_multiple_rois(test_data_path):
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with RawFile(test_data_path / "raw/ROITestData/MultipleROIs/run_master_0.json") as f:
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num_rois = f.num_rois
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#cannot read_frame for multiple ROIs
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with pytest.raises(RuntimeError):
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f.read_frame()
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assert f.tell() == 0
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_, frames = f.read_rois()
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assert num_rois == 2
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assert len(frames) == 2
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assert frames[0].shape == (301, 101)
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assert frames[1].shape == (101, 101)
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assert f.tell() == 1
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# read multiple ROIs at once
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_, frames = f.read_n_with_roi(2, roi_index = 1)
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assert frames.shape == (2, 101, 101)
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assert f.tell() == 3
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f.seek(1)
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# read specific ROI
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_, frame = f.read_roi(0)
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assert frame.shape == (301, 101)
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assert f.tell() == 2
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@pytest.mark.withdata
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def test_read_rawfile_quad_eiger_and_compare_to_numpy(test_data_path):
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d0 = test_data_path/'raw/eiger_quad_data/W13_vrpreampscan_m21C_300V_800eV_vthre2000_d0_f0_0.raw'
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d1 = test_data_path/'raw/eiger_quad_data/W13_vrpreampscan_m21C_300V_800eV_vthre2000_d1_f0_0.raw'
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image = np.zeros((512,512), dtype=np.uint32)
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with open(d0) as f:
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raw = np.fromfile(f, dtype=np.uint32, count = 256*512, offset = 20*256*512*4 + 112*21).reshape(256,512)
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image[256:,:] = raw
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with open(d1) as f:
|
|
raw = np.fromfile(f, dtype=np.uint32, count = 256*512, offset = 20*256*512*4 + 112*21).reshape(256,512)
|
|
|
|
image[0:256,:] = raw[::-1,:]
|
|
|
|
with RawFile(test_data_path/'raw/eiger_quad_data/W13_vrpreampscan_m21C_300V_800eV_vthre2000_master_0.json') as f:
|
|
f.seek(20)
|
|
header, image1 = f.read_frame()
|
|
|
|
assert (image == image1).all()
|
|
|
|
@pytest.mark.withdata
|
|
def test_read_rawfile_eiger_and_compare_to_numpy(test_data_path):
|
|
d0 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d0_f0_7.raw'
|
|
d1 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d1_f0_7.raw'
|
|
d2 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d2_f0_7.raw'
|
|
d3 = test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_d3_f0_7.raw'
|
|
|
|
image = np.zeros((512,1024), dtype=np.uint32)
|
|
|
|
#TODO why is there no header offset?
|
|
with open(d0) as f:
|
|
raw = np.fromfile(f, dtype=np.uint32, count = 256*512, offset=112).reshape(256,512)
|
|
|
|
image[0:256,0:512] = raw[::-1]
|
|
|
|
with open(d1) as f:
|
|
raw = np.fromfile(f, dtype=np.uint32, count = 256*512, offset=112).reshape(256,512)
|
|
|
|
image[0:256,512:] = raw[::-1]
|
|
|
|
with open(d2) as f:
|
|
raw = np.fromfile(f, dtype=np.uint32, count = 256*512, offset=112).reshape(256,512)
|
|
|
|
image[256:,0:512] = raw
|
|
|
|
with open(d3) as f:
|
|
raw = np.fromfile(f, dtype=np.uint32, count = 256*512, offset=112).reshape(256,512)
|
|
|
|
image[256:,512:] = raw
|
|
|
|
|
|
with RawFile(test_data_path/'raw/eiger/Lab6_20500eV_2deg_20240629_master_7.json') as f:
|
|
header, image1 = f.read_frame()
|
|
|
|
assert (image == image1).all()
|
|
|
|
|
|
@pytest.mark.withdata
|
|
def test_read_eiger_udp_port_disabled(test_data_path):
|
|
with RawFile(test_data_path / "raw/eiger/one_udp_port_disabled_master_0.json") as f:
|
|
_, frame = f.read_rois()
|
|
|
|
assert(len(frame) == 2)
|
|
assert frame[0].shape == (256, 512)
|
|
assert frame[1].shape == (256, 1024)
|
|
assert f.master.udp_port_types == [UDPPortPosition.LEFT, UDPPortPosition.RIGHT]
|
|
rois = f.master.rois
|
|
assert len(rois) == 2
|
|
assert rois[0] == ROI(512, 1024, 0, 256)
|
|
assert rois[1] == ROI(0, 1024, 256, 512)
|
|
|
|
with RawFile(test_data_path / "raw/eiger/quad_eiger_disabled_bottom_port_master_0.json") as f:
|
|
_, frame = f.read_frame()
|
|
|
|
assert frame.shape == (256, 512)
|
|
assert(f.master.disabled_udp_ports == [1])
|
|
assert f.master.udp_port_types == [UDPPortPosition.TOP, UDPPortPosition.BOTTOM]
|
|
rois = f.master.rois
|
|
assert len(rois) == 1
|
|
assert rois[0] == ROI(0, 512, 256, 512)
|
|
|
|
with RawFile(test_data_path / "raw/eiger/2_modules_eiger_disabled_udp_port_master_0.json") as f:
|
|
_, frame = f.read_rois()
|
|
|
|
assert(len(frame) == 2)
|
|
assert frame[0].shape == (512, 512)
|
|
assert frame[1].shape == (512, 512)
|
|
assert (f.master.disabled_udp_ports == [1, 3, 5, 7])
|
|
assert f.master.udp_port_types == [UDPPortPosition.LEFT, UDPPortPosition.RIGHT]
|
|
rois = f.master.rois
|
|
assert len(rois) == 2
|
|
assert rois[0] == ROI(0, 512, 0, 512)
|
|
assert rois[1] == ROI(1024, 1536, 0, 512)
|
|
|
|
|
|
@pytest.mark.parametrize("layout", [(1, 1), (2, 1), (1, 2), (2, 2), (3, 2)])
|
|
@pytest.mark.parametrize("reader_type", [RawFile, File])
|
|
def test_raw_file_assembles_module_layout(tmp_path, layout, reader_type):
|
|
layout_rows, layout_cols = layout
|
|
master_path, expected = write_module_layout(tmp_path, layout_rows, layout_cols)
|
|
|
|
with reader_type(master_path) as reader:
|
|
# RawFile binds rows/cols as methods (ROI overloads), File as properties
|
|
rows = reader.rows() if reader_type is RawFile else reader.rows
|
|
cols = reader.cols() if reader_type is RawFile else reader.cols
|
|
assert (rows, cols) == expected.shape
|
|
result = reader.read_frame()
|
|
image = result[1] if reader_type is RawFile else result
|
|
assert image.shape == expected.shape
|
|
assert (image == expected).all()
|
|
|
|
reader.seek(0)
|
|
result = reader.read_n(2)
|
|
images = result[1] if reader_type is RawFile else result
|
|
assert images.shape == (2,) + expected.shape
|
|
assert (images == expected).all()
|
|
|
|
|
|
@pytest.mark.parametrize("layout", [(1, 1), (2, 1), (1, 2)])
|
|
def test_raw_file_gap_pixels(tmp_path, layout):
|
|
layout_rows, layout_cols = layout
|
|
master_path, expected = write_module_layout(tmp_path, layout_rows, layout_cols,
|
|
module_rows=512, module_cols=1024)
|
|
gaps = GapPixels(fill_value=5)
|
|
with RawFile(master_path, gap_pixels=gaps) as reader:
|
|
assert reader.gap_pixels == gaps
|
|
# one chip boundary per module row, three per module column and no
|
|
# gap between modules
|
|
assert (reader.rows(), reader.cols()) == ((512 + 2) * layout_rows, (1024 + 6) * layout_cols)
|
|
header, image = reader.read_frame()
|
|
assert header.size == layout_rows * layout_cols
|
|
assert (image == insert_gap_pixels(expected, gaps)).all()
|
|
reader.seek(0)
|
|
_, images = reader.read_n(2)
|
|
assert images.shape == (2, reader.rows(), reader.cols())
|
|
assert (images[1] == image).all()
|
|
|
|
with RawFile(master_path) as reader:
|
|
assert reader.gap_pixels is None
|
|
assert (reader.rows(), reader.cols()) == expected.shape
|
|
|
|
with RawFile(master_path, gap_pixels=True) as reader:
|
|
assert reader.gap_pixels == GapPixels()
|
|
assert (reader.rows(), reader.cols()) == insert_gap_pixels(expected).shape
|
|
_, image = reader.read_frame()
|
|
assert (image == insert_gap_pixels(expected)).all()
|
|
|
|
module_gaps = GapPixels(module_gaps=ModuleGaps(8, 36))
|
|
with RawFile(master_path, gap_pixels=module_gaps) as reader:
|
|
assert (reader.rows(), reader.cols()) == insert_gap_pixels(expected, module_gaps).shape
|
|
_, image = reader.read_frame()
|
|
assert (image == insert_gap_pixels(expected, module_gaps)).all()
|
|
|
|
|
|
def test_raw_file_gap_pixels_split_counts(tmp_path):
|
|
# one Eiger module: four 256x512 ports in a 2x2 layout. Splitting is
|
|
# rejected on raw Jungfrau data. The plain read is the reference since
|
|
# Eiger ports are row flipped on reading.
|
|
master_path, _ = write_module_layout(tmp_path, 2, 2, module_rows=256, module_cols=512,
|
|
detector_type="Eiger")
|
|
gaps = GapPixels(split_counts=True, seed=11)
|
|
with RawFile(master_path) as reader:
|
|
_, plain = reader.read_frame()
|
|
with RawFile(master_path, gap_pixels=gaps) as reader:
|
|
_, image = reader.read_frame()
|
|
assert (image == insert_gap_pixels(plain, gaps)).all()
|
|
assert image.sum() == plain.sum()
|
|
|
|
|
|
def test_raw_file_gap_pixels_split_counts_rejected_for_jungfrau(tmp_path):
|
|
master_path, _ = write_module_layout(tmp_path, 1, 1, module_rows=512, module_cols=1024)
|
|
RawFile(master_path, gap_pixels=GapPixels())
|
|
with pytest.raises(ValueError):
|
|
RawFile(master_path, gap_pixels=GapPixels(split_counts=True))
|
|
|
|
|
|
def test_raw_file_gap_pixels_unsupported_detector(tmp_path):
|
|
master_path, _ = write_module_layout(tmp_path, 1, 1, detector_type="Moench")
|
|
RawFile(master_path)
|
|
with pytest.raises(ValueError):
|
|
RawFile(master_path, gap_pixels=True)
|
|
|
|
|
|
@pytest.mark.withdata
|
|
def test_raw_file_gap_pixels_recorded_jungfrau(test_data_path):
|
|
path = test_data_path / "raw/jungfrau/jungfrau_single_master_0.json"
|
|
gaps = GapPixels(fill_value=3)
|
|
with RawFile(path, gap_pixels=gaps) as gapped, RawFile(path) as plain:
|
|
assert (gapped.rows(), gapped.cols()) == (514, 1030)
|
|
_, image = gapped.read_frame()
|
|
_, reference = plain.read_frame()
|
|
assert image.shape == (514, 1030)
|
|
assert (image == insert_gap_pixels(reference, gaps)).all()
|
|
|
|
|
|
@pytest.mark.withdata
|
|
def test_raw_file_gap_pixels_recorded_rois(test_data_path):
|
|
path = test_data_path / "raw/ROITestData/MultipleROIs/run_master_0.json"
|
|
with RawFile(path, gap_pixels=True) as gapped, RawFile(path) as plain:
|
|
assert gapped.num_rois == 2
|
|
_, images = gapped.read_rois()
|
|
_, references = plain.read_rois()
|
|
rois = plain.master.rois
|
|
assert images[0].shape == (303, 103)
|
|
assert images[1].shape == (101, 103)
|
|
for image, reference, roi in zip(images, references, rois):
|
|
assert (image == insert_gap_pixels(reference, roi=roi)).all()
|
|
gapped.seek(0)
|
|
_, frames = gapped.read_n_with_roi(2, roi_index=1)
|
|
assert frames.shape == (2, 101, 103)
|