Edge align Function created (#943)

* Added edge_align plan for beam edge alignment * Need to find a better way to check signal quality. * Formatted using ruff * small formatting changes * removed unused stats import * removed another unused import * Added a check function that yields correct results * intermediate commit saving progress * finished try/except when bad signal is detected * Fixed formatting * Added scipy to environment.yaml & requirements.txt * CI #909 switch to 'ruff' * DOC #909 update release notes * MNT #909 revise per 'ruff check' * CI #909 update * Bump davidslusser/actions_python_ruff from 1.0.0 to 1.0.1 Bumps [davidslusser/actions_python_ruff](https://github.com/davidslusser/actions_python_ruff) from 1.0.0 to 1.0.1. - [Release notes](https://github.com/davidslusser/actions_python_ruff/releases) - [Commits](davidslusser/actions_python_ruff@v1.0.0...v1.0.1) --- updated-dependencies: - dependency-name: davidslusser/actions_python_ruff dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> * MNT #872 hoist from MPE devices * TST #872 adjust for new hoist * MNT #872 * MNT #872 refactor * MNT #872 hoist utils * DOC #912 * ENV #938 bump the minimum requirement * DOC #932 update relase notes * DOC #938 contribution from @sveseli * MNT #914 setup.py --> pyproject.toml * DOC #921 copyright year * MNT #914 * Added edge_align function for beam edge alignment * added scipy to pyproject.toml * CI #909 switch to 'ruff' * DOC badge * DOC badge * DOC #940 example scans with sscan record * DOC #940 it's only a word ... * DOC #940 * DOC #940 it's a demo, actually * DOC #940 * DOC #940 convert the blocking call to st.wait() * DOC #940 per review * DOC #940 per review * DOC #940 proofreading * DOC #940 per review, remove the section with the polling loop * DOC #940 new title * DOC #940 more proofing * DOC #940 clarify the default sscan record array size of 1,000 * DOC #940 refactor to polling loop. Show the recommended style in a details section. * DOC #940 * Added put_complete=True to sensitivity value and unit for the SRS-570 Pre-amp. * Added a test for the sensitivity_unit put_complete, and removed the put_complete from sensitivity_value. * CI #955 move requirements file * MNT #955 sphinx config * DOC #955 re-arrange * DOC #955 apply to lower-level pages * DOC #955 add docs upload * CI #955 * CI #955 * CI #955 wip * CI #955 * CI #955 * DOC #917 release note * DOC #957 merge overview into home page * DOC #955 * DOC #955 * DOC #955 * DOC #955 * Added edge_align function for beam edge alignment * Added edge_align function for beam edge alignment * Added edge_align function for beam edge alignment * DOC #909 update release notes * DOC #932 update relase notes * Added edge_align function for beam edge alignment * CI #909 switch to 'ruff' * DOC #955 * Fixed merge issue * fixed unused import * change for tests to pass * Formatting changes * Fixed repeated section * Small formatting changes * Small syntax change * Added toolz & scipy to conf.py --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Codrea <[email protected]> Co-authored-by: Pete R Jemian <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Pete R Jemian <[email protected]> Co-authored-by: Mark Wolfman <[email protected]>
BCDA-APS · Apr 12, 2024 · af11141 · af11141
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diff --git a/.ruff.toml b/.ruff.toml
@@ -0,0 +1,81 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 115
+indent-width = 4
+
+# Assume Python 3.8
+target-version = "py38"
+
+[lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F"]
+ignore = ["E402", "E741", "F405"]
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[lint.per-file-ignores]
+"__init__.py" = ["F401", "F403"]
+"**/{tests,docs,tools}/*" = ["E402"]
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = false
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -31,10 +31,11 @@ describe future plans.
 release expected by 2024-04-12
 
 New Features
- ------------
+------------
+
+* Add new plan for edge alignment called edge_align
+* Added a mesh grid scan plan that will collect until number of collection points is met
 
- * Added a mesh grid scan plan that will collect until number of collection points is met
-
 Fixes
 -----
 

diff --git a/apstools/plans/__init__.py b/apstools/plans/__init__.py
@@ -2,6 +2,7 @@
 from .alignment import TuneResults
 from .alignment import lineup
 from .alignment import lineup2
+from .alignment import edge_align
 from .alignment import tune_axes
 from .command_list import CommandFileReadError
 from .command_list import command_list_as_table

diff --git a/apstools/plans/alignment.py b/apstools/plans/alignment.py
@@ -16,6 +16,9 @@
 
 import numpy as np
 import pyRestTable
+from scipy.optimize import curve_fit
+from scipy.special import erf
+
 from bluesky import plan_stubs as bps
 from bluesky import plans as bp
 from bluesky import preprocessors as bpp
@@ -213,6 +216,115 @@ def peak_analysis():
         scaler.stage_sigs = old_sigs
 
 
+def edge_align(detectors, mover, start, end, points, cat=None, md={}):
+    """
+    Align to the edge given mover & detector data, relative to absolute position.
+
+    This plan can be used in the queueserver, Jupyter notebooks, and IPython
+    consoles.
+
+    PARAMETERS
+    ----------
+    detectors *Readable* or [*Readable*]:
+        Detector object or list of detector objects (each is a Device or
+        Signal).
+
+    mover *Movable*:
+        Mover object, such as motor or other positioner.
+
+    start *float*:
+        Starting point for the scan. This is an absolute motor location.
+
+    end *float*:
+        Ending point for the scan. This is an absolute motor location.
+
+    points *int*:
+        Number of points in the scan.
+
+    cat *databroker.temp().v2*:
+        Catalog where bluesky data is saved and can be retrieved from.
+
+    md *dict*:
+        User-supplied metadata for this scan.
+    """
+
+    def guess_erf_params(x_data, y_data):
+        """
+        Provide an initial guess for the parameters of an error function.
+
+        Parameters
+        ----------
+        x_data : A numpy array of the values on the x_axis
+        y_data : A numpy array of the values on the y_axis
+
+        Returns
+        -------
+        guess : dict
+            A dictionary containing the guessed parameters 'low_y_data', 'high_y_data', 'width', and 'midpoint'.
+        """
+
+        # Sort data to make finding the mid-point easier and to assist in other estimations
+        y_data_sorted = np.sort(y_data)
+        x_data_sorted = np.sort(x_data)
+
+        # Estimate low and high as the first and last elements (assuming sorted data)
+        low_y_data = np.min(y_data_sorted)
+        high_y_data = np.max(y_data_sorted)
+
+        low_x_data = np.min(x_data_sorted)
+        high_x_data = np.max(x_data_sorted)
+
+        # Estimate wid as a fraction of the range. This is very arbitrary and might need tuning!
+        width = (
+            high_x_data - low_x_data
+        ) / 10  # This is a guess and might need adjustment based on your data's characteristics
+
+        # Estimate the midpoint of the x values
+        midpoint = x_data[int(len(x_data) / 2)]
+
+        return [low_y_data, high_y_data, width, midpoint]
+
+    def erf_model(x, low, high, width, midpoint):
+        """
+        Create error function for fitting and simulation
+
+        Parameters
+        ----------
+        x		:	input upon which error function is evaluated
+        low		: 	min value of error function
+        high	: 	max value of error function
+        width  	:	"spread" of error function transition region
+        midpoint:	location of error function's "center"
+        """
+        return (high - low) * 0.5 * (1 - erf((x - midpoint) / width)) + low
+
+    if not isinstance(detectors, (tuple, list)):
+        detectors = [detectors]
+
+    _md = dict(purpose="edge_align")
+    _md.update(md or {})
+
+    uid = yield from bp.scan(detectors, mover, start, end, points, md=_md)
+    cat = cat or utils.getCatalog()
+    run = cat[uid]  # return uids
+    ds = run.primary.read()
+
+    x = ds["mover"]
+    y = ds["noisy"]
+
+    try:
+        initial_guess = guess_erf_params(x, y)
+        popt, pcov = curve_fit(erf_model, x, y, p0=initial_guess)
+        if pcov[3, 3] != np.inf:
+            print("Significant signal change detected; motor moving to detected edge.")
+            yield from bps.mv(mover, popt[3])
+        else:
+            raise Exception
+    except Exception as reason:
+        print(f"reason: {reason}")
+        print("No significant signal change detected; motor movement skipped.")
+
+
 def lineup2(
     # fmt: off
     detectors, mover, rel_start, rel_end, points,

diff --git a/docs/source/api/_plans.rst b/docs/source/api/_plans.rst
@@ -31,6 +31,7 @@ Custom Scans
 
 .. autosummary::
 
+   ~apstools.plans.alignment.edge_align
    ~apstools.plans.alignment.lineup
    ~apstools.plans.alignment.lineup2
    ~apstools.plans.alignment.tune_axes

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -110,6 +110,8 @@
     psutil
     pyRestTable
     pysumreg
+    scipy
     spec2nexus
+    toolz
     xarray
 """.split()
diff --git a/environment.yml b/environment.yml
@@ -31,6 +31,7 @@ dependencies:
   - pysumreg
   - qt =5
   - readline !=8.1.2
+  - scipy
   - setuptools-scm
   - spec2nexus
   - sphinx >=5

diff --git a/pyproject.toml b/pyproject.toml
@@ -67,6 +67,7 @@ dependencies = [
   "pyepics>=3.4.2",
   "pyRestTable>=2020.0.8",
   "pysumreg",
+  "scipy",
   "spec2nexus>=2021.1.7",
   "toolz>=0.12.1",
   "xlrd",

diff --git a/requirements.txt b/requirements.txt
@@ -13,5 +13,6 @@ psutil
 pyepics>=3.4.2
 pyRestTable
 pysumreg
+scipy
 spec2nexus>=2021.1.7
 xlrd