Developer (#164)

- State before merging the new cluster vector API

---------

Co-authored-by: Patrick <patrick.sieberer@psi.ch>
Co-authored-by: JulianHeymes <julian.heymes@psi.ch>
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
Co-authored-by: Xiangyu Xie <45243914+xiangyuxie@users.noreply.github.com>
Co-authored-by: xiangyu.xie <xiangyu.xie@psi.ch>
Co-authored-by: siebsi <sieb.patr@gmail.com>

python/tests/conftest.py

@@ -0,0 +1,29 @@
+import os
+from pathlib import Path
+import pytest
+
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--files", action="store_true", default=False, help="run slow tests"
+    )
+
+
+def pytest_configure(config):
+    config.addinivalue_line("markers", "files: mark test as needing image files to run")
+
+
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--files"):
+        return
+    skip = pytest.mark.skip(reason="need --files option to run")
+    for item in items:
+        if "files" in item.keywords:
+            item.add_marker(skip)
+
+
+@pytest.fixture
+def test_data_path():
+    return Path(os.environ["AARE_TEST_DATA"])
+

python/tests/test_RawSubFile.py

@@ -0,0 +1,36 @@
+import pytest
+import numpy as np
+from aare import RawSubFile, DetectorType
+
+
+@pytest.mark.files
+def test_read_a_jungfrau_RawSubFile(test_data_path):
+    with RawSubFile(test_data_path / "raw/jungfrau/jungfrau_single_d0_f1_0.raw", DetectorType.Jungfrau, 512, 1024, 16) as f:
+        assert f.frames_in_file == 3
+
+        headers, frames = f.read()
+
+    assert headers.size == 3
+    assert frames.shape == (3, 512, 1024)
+    
+    # Frame numbers in this file should be 4, 5, 6
+    for i,h in zip(range(4,7,1), headers):
+        assert h["frameNumber"] == i
+
+    # Compare to canned data using numpy
+    data = np.load(test_data_path / "raw/jungfrau/jungfrau_single_0.npy")
+    assert np.all(data[3:6] == frames)
+
+@pytest.mark.files
+def test_iterate_over_a_jungfrau_RawSubFile(test_data_path):
+
+    data = np.load(test_data_path / "raw/jungfrau/jungfrau_single_0.npy")
+
+    with RawSubFile(test_data_path / "raw/jungfrau/jungfrau_single_d0_f0_0.raw", DetectorType.Jungfrau, 512, 1024, 16) as f:
+        i = 0
+        for header, frame in f:
+            assert header["frameNumber"] == i+1
+            assert np.all(frame == data[i])
+            i += 1
+        assert i == 3
+        assert header["frameNumber"] == 3

python/tests/test_jungfrau_dat_files.py

@@ -0,0 +1,92 @@
+import pytest
+import numpy as np
+from aare import JungfrauDataFile
+
+@pytest.mark.files
+def test_jfungfrau_dat_read_number_of_frames(test_data_path):
+    with JungfrauDataFile(test_data_path / "dat/AldoJF500k_000000.dat") as dat_file:
+        assert dat_file.total_frames == 24
+
+    with JungfrauDataFile(test_data_path / "dat/AldoJF250k_000000.dat") as dat_file:
+        assert dat_file.total_frames == 53
+    
+    with JungfrauDataFile(test_data_path / "dat/AldoJF65k_000000.dat") as dat_file:
+        assert dat_file.total_frames == 113
+
+
+@pytest.mark.files
+def test_jfungfrau_dat_read_number_of_file(test_data_path):
+    with JungfrauDataFile(test_data_path / "dat/AldoJF500k_000000.dat") as dat_file:
+        assert dat_file.n_files == 4
+
+    with JungfrauDataFile(test_data_path / "dat/AldoJF250k_000000.dat") as dat_file:
+        assert dat_file.n_files == 7
+    
+    with JungfrauDataFile(test_data_path / "dat/AldoJF65k_000000.dat") as dat_file:
+        assert dat_file.n_files == 7
+
+
+@pytest.mark.files
+def test_read_module(test_data_path):
+    """
+    Read all frames from the series of .dat files. Compare to canned data in npz format. 
+    """
+
+    # Read all frames from the .dat file
+    with JungfrauDataFile(test_data_path / "dat/AldoJF500k_000000.dat") as f:
+        header, data = f.read()
+
+    #Sanity check
+    n_frames = 24
+    assert header.size == n_frames
+    assert data.shape == (n_frames, 512, 1024)
+
+    # Read reference data using numpy
+    with np.load(test_data_path / "dat/AldoJF500k.npz") as f:
+        ref_header = f["headers"]
+        ref_data = f["frames"]
+
+    # Check that the data is the same
+    assert np.all(ref_header == header)
+    assert np.all(ref_data == data)
+
+@pytest.mark.files
+def test_read_half_module(test_data_path):
+
+    # Read all frames from the .dat file
+    with JungfrauDataFile(test_data_path / "dat/AldoJF250k_000000.dat") as f:
+        header, data = f.read()
+
+    n_frames = 53
+    assert header.size == n_frames
+    assert data.shape == (n_frames, 256, 1024)
+
+    # Read reference data using numpy
+    with np.load(test_data_path / "dat/AldoJF250k.npz") as f:
+        ref_header = f["headers"]
+        ref_data = f["frames"]
+
+    # Check that the data is the same
+    assert np.all(ref_header == header)
+    assert np.all(ref_data == data)
+
+
+@pytest.mark.files
+def test_read_single_chip(test_data_path):
+
+    # Read all frames from the .dat file
+    with JungfrauDataFile(test_data_path / "dat/AldoJF65k_000000.dat") as f:
+        header, data = f.read()
+
+    n_frames = 113
+    assert header.size == n_frames
+    assert data.shape == (n_frames, 256, 256)
+
+    # Read reference data using numpy
+    with np.load(test_data_path / "dat/AldoJF65k.npz") as f:
+        ref_header = f["headers"]
+        ref_data = f["frames"]
+
+    # Check that the data is the same
+    assert np.all(ref_header == header)
+    assert np.all(ref_data == data)