Merge pull request #18 from pylhc/doros_lhc

Reader/writer for DOROS BPM data

.gitignore

@@ -71,6 +71,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+doc/_build/
 doc_build/
 
 # PyBuilder

doc/conf.py

@@ -11,16 +11,21 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
 import pathlib
 import sys
 
 # ignore numpy warnings, see:
 # https://stackoverflow.com/questions/40845304/runtimewarning-numpy-dtype-size-changed-may-indicate-binary-incompatibility
 import warnings
 
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
+warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
+
 
 TOPLEVEL_DIR = pathlib.Path(__file__).parent.parent.absolute()
 ABOUT_FILE = TOPLEVEL_DIR / "turn_by_turn" / "__init__.py"
@@ -63,6 +68,8 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
     "sphinx.ext.githubpages",
     "sphinx.ext.napoleon",
 ]
+autosectionlabel_prefix_document = True
+autosectionlabel_maxdepth = 2
 
 # Add any paths that contain templates here, relative to this directory.
 # templates_path = ['_templates']
@@ -78,7 +85,7 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
 
 # General information about the project.
 project = ABOUT_TBT["__title__"]
-copyright_ = "2018-2021, pyLHC/OMC-TEAM"
+copyright_ = "2018-2024, pyLHC/OMC-TEAM"
 author = ABOUT_TBT["__author__"]
 
 # Override link in 'Edit on Github'
@@ -100,7 +107,7 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -120,13 +127,6 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
 #
 html_theme = "sphinx_rtd_theme"
 
-html_theme_options = {
-    "collapse_navigation": False,
-    "display_version": True,
-    "logo_only": True,
-    "navigation_depth": 2,
-}
-
 html_logo = "_static/img/omc_logo.svg"
 html_static_path = ["_static"]
 html_context = {
@@ -147,13 +147,28 @@ def about_package(init_posixpath: pathlib.Path) -> dict:
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
+html_theme_options = {
+    'collapse_navigation': False,
+    'display_version': True,
+    'logo_only': True,
+    'navigation_depth': 1,
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 # html_static_path = ['_static']
 
+# A dictionary of values to pass into the template engine’s context for all
+# pages. Single values can also be put in this dictionary using the
+# -A command-line option of sphinx-build.
+html_context = {
+    'display_github': True,
+    # the following are only needed if :github_url: is not set
+    'github_user': author,
+    'github_repo': project,
+    'github_version': 'master/doc/',
+}
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #

doc/modules/index.rst

@@ -1,15 +1,19 @@
 .. automodule:: turn_by_turn.constants
     :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.io
     :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.structures
     :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.utils
     :members:
+    :noindex:
 

doc/readers/index.rst

@@ -1,19 +1,33 @@
+.. automodule:: turn_by_turn.doros
+    :members:
+    :noindex:
+
+
 .. automodule:: turn_by_turn.esrf
     :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.iota
     :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.lhc
     :members:
+    :noindex:
+
+
+.. automodule:: turn_by_turn.sps
+    :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.ptc
     :members:
+    :noindex:
 
 
 .. automodule:: turn_by_turn.trackone
     :members:
-
+    :noindex:

pyproject.toml

@@ -16,7 +16,7 @@ exclude = [
 packages = ["turn_by_turn"]
 
 [project]
-name = "tfs-turn_by_turn"
+name = "turn_by_turn"
 readme = "README.md"
 description = "Read and write turn-by-turn measurement files from different particle accelerator formats."
 authors = [

tests/test_doros.py

@@ -0,0 +1,115 @@
+
+from datetime import datetime
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import pytest
+import h5py
+
+from turn_by_turn.constants import PRINT_PRECISION
+from turn_by_turn.errors import DataTypeError
+from turn_by_turn.structures import TbtData, TransverseData
+from tests.test_lhc_and_general import create_data, compare_tbt
+
+from turn_by_turn.doros import N_ORBIT_SAMPLES, read_tbt, write_tbt, DEFAULT_BUNCH_ID, POSITIONS
+
+INPUTS_DIR = Path(__file__).parent / "inputs"
+
+
+def test_read_write_real_data(tmp_path):
+    tbt = read_tbt(INPUTS_DIR / "test_doros.h5", bunch_id=10)
+
+    assert tbt.nbunches == 1
+    assert len(tbt.matrices) == 1
+    assert tbt.nturns == 50000
+    assert tbt.matrices[0].X.shape == (3, tbt.nturns)
+    assert tbt.matrices[0].Y.shape == (3, tbt.nturns)
+    assert len(set(tbt.matrices[0].X.index)) == 3
+    assert np.all(tbt.matrices[0].X.index == tbt.matrices[0].Y.index)
+
+    file_path = tmp_path / "test_file.h5"
+    write_tbt(tbt, file_path)
+    new = read_tbt(file_path, bunch_id=10)
+    compare_tbt(tbt, new, no_binary=False)
+
+
+def test_write_read(tmp_path):
+    tbt = _tbt_data()
+    file_path = tmp_path / "test_file.h5"
+    write_tbt(tbt, file_path)
+    new = read_tbt(file_path)
+    compare_tbt(tbt, new, no_binary=False)
+
+
+def test_read_raises_different_bpm_lengths(tmp_path):
+    tbt = _tbt_data()
+    file_path = tmp_path / "test_file.h5"
+    write_tbt(tbt, file_path)
+
+    bpm = tbt.matrices[0].X.index[0]
+
+    # modify the BPM lengths in the file
+    with h5py.File(file_path, "r+") as h5f:
+        delta = 10
+        del h5f[bpm][N_ORBIT_SAMPLES]
+        h5f[bpm][N_ORBIT_SAMPLES] = [tbt.matrices[0].X.shape[1] - delta]
+        for key in POSITIONS.values():
+            data = h5f[bpm][key][:-delta]
+            del h5f[bpm][key]
+            h5f[bpm][key] = data
+
+    with pytest.raises(ValueError) as e:
+        read_tbt(file_path)
+    assert "Not all BPMs have the same number of turns!" in str(e)
+
+
+def test_read_raises_on_different_bpm_lengths_in_data(tmp_path):
+    tbt = _tbt_data()
+    file_path = tmp_path / "test_file.h5"
+    write_tbt(tbt, file_path)
+
+    bpms = [tbt.matrices[0].X.index[i] for i in (0, 2)]
+
+    # modify the BPM lengths in the file
+    with h5py.File(file_path, "r+") as h5f:
+        for bpm in bpms:
+            del h5f[bpm][N_ORBIT_SAMPLES]
+            h5f[bpm][N_ORBIT_SAMPLES] = [tbt.matrices[0].X.shape[1] + 10]
+
+    with pytest.raises(ValueError) as e:
+        read_tbt(file_path)
+    assert "Found BPMs with different data lengths" in str(e)
+    assert all(bpm in str(e) for bpm in bpms)
+
+
+def _tbt_data() -> TbtData:
+    """TbT data for testing. Adding random noise, so that the data is different per BPM."""
+    nturns = 2000
+    bpms = ["TBPM1", "TBPM2", "TBPM3", "TBPM4"]
+
+    return TbtData(
+        matrices=[
+            TransverseData(
+                X=pd.DataFrame(
+                    index=bpms,
+                    data=create_data(
+                        np.linspace(-np.pi, np.pi, nturns, endpoint=False), 
+                        nbpm=len(bpms), function=np.sin, noise=0.02
+                    ),
+                    dtype=float,
+                ),
+                Y=pd.DataFrame(
+                    index=bpms,
+                    data=create_data(
+                        np.linspace(-np.pi, np.pi, nturns, endpoint=False), 
+                        nbpm=len(bpms), function=np.cos, noise=0.015
+                    ),
+                    dtype=float,
+                ),
+            )
+        ],
+        date=datetime.now(),
+        bunch_ids=[DEFAULT_BUNCH_ID],
+        nturns=nturns,
+    )

tests/test_lhc_and_general.py

@@ -72,8 +72,8 @@ def compare_tbt(origin: TbtData, new: TbtData, no_binary: bool, max_deviation =
                 assert np.all(origin_mat == new_mat)
 
 
-def create_data(phases, nbpm, function) -> np.ndarray:
-    return np.ones((nbpm, len(phases))) * function(phases)
+def create_data(phases, nbpm, function, noise: float = 0) -> np.ndarray:
+    return np.ones((nbpm, len(phases))) * function(phases) + noise * np.random.randn(nbpm, len(phases))
 
 
 @pytest.fixture()

turn_by_turn/__init__.py

@@ -5,7 +5,7 @@
 __title__ = "turn_by_turn"
 __description__ = "Read and write turn-by-turn measurement files from different particle accelerator formats."
 __url__ = "https://github.com/pylhc/turn_by_turn"
-__version__ = "0.6.0"
+__version__ = "0.7.0"
 __author__ = "pylhc"
 __author_email__ = "pylhc@github.com"
 __license__ = "MIT"