Patch 1.1.1 (#100)

docker/environment.yml

@@ -200,7 +200,7 @@ dependencies:
   - stack_data=0.2.0
   - statsmodels=0.13.2
   - sympy=1.9
-  - tfs-pandas=3.1.0
+  - tfs-pandas=3.2.1
   - threadpoolctl=3.1.0
   - tk=8.6.12
   - tomli=2.0.1
@@ -225,6 +225,6 @@ dependencies:
     - importlib-resources==5.4.0
     - minrpc==0.1.0
     - optics-functions==0.1.2
-    - pyhdtoolkit==1.1.0
+    - pyhdtoolkit==1.1.1
     - pynaff==1.1.4
-    - scipy==1.9.0
+    - scipy==1.9.3

docs/release.rst

@@ -3,6 +3,14 @@ Release Notes
 
 The full list of releases can be found in the GitHub repository's `releases page <https://github.com/fsoubelet/PyhDToolkit/releases>`_.
 
+Version 1.1.1
+-------------
+
+.. toctree::
+    :maxdepth: 2
+
+    releases/v1.1.1
+
 Version 1.1.0
 -------------
 

docs/releases/v1.1.1.rst

@@ -0,0 +1,16 @@
+.. _release_1.1.1:
+
+1.1.1
+-----
+
+Release `1.1.1` brings a few fixes and settings changes.
+
+Bug Fixes
+~~~~~~~~~
+
+* Various functions in the `~pyhdtoolkit.cpymadtools` submodules do not use the ``CHROM`` flag by default (in ``TWISS`` or matching routines). Providing ``CHROM`` is still possible through ``kwargs``.
+* Many calls to `.copy()` following a call to `.dframe()` when querying a ``MAD-X`` table have been removed, as they were redundant.
+* A few values in the available plotting settings were changed.
+
+
+See `v1.1.1 release notes on GitHub <https://github.com/fsoubelet/PyhDToolkit/releases/tag/1.1.1>`_ and the `full changes since v1.0.0 <https://github.com/fsoubelet/PyhDToolkit/compare/1.1.0...1.1.1>`_.

examples/demo_aperture.py

@@ -48,7 +48,7 @@
 # We can now determine the exact position of the IP5 point and plot the LHC
 # injection aperture:
 
-twiss_df = madx.table.twiss.dframe().copy()
+twiss_df = madx.table.twiss.dframe()
 ip5s = twiss_df.s[twiss_df.name.str.contains("ip5")].to_numpy()[0]
 
 ###############################################################################

examples/demo_ir_errors.py

@@ -72,7 +72,7 @@
 
 madx.command.use(sequence="lhcb1")
 matching.match_tunes_and_chromaticities(madx, "lhc", "lhcb1", 62.31, 60.32, 2.0, 2.0)
-error_table = madx.table.ir_quads_errors.dframe().copy()
+error_table = madx.table.ir_quads_errors.dframe()
 
 ###############################################################################
 # Let's quickly re-arrange the resulting `~pandas.DataFrame` to align with the

examples/demo_lattice.py

@@ -89,7 +89,7 @@
 # of points of interest through the ``TWISS`` table:
 
 lhc_madx.command.twiss()
-twiss_df = lhc_madx.table.twiss.dframe().copy()
+twiss_df = lhc_madx.table.twiss.dframe()
 twiss_df.name = twiss_df.name.apply(lambda x: x[:-2])
 ip1s = twiss_df.s["ip1"]
 

examples/demo_lhc_rigid_waist_shift.py

@@ -57,7 +57,7 @@
 # determine the position of points of interest through the ``TWISS`` table:
 
 madx.command.twiss()
-twiss_df = madx.table.twiss.dframe().copy()
+twiss_df = madx.table.twiss.dframe()
 twiss_df.name = twiss_df.name.apply(lambda x: x[:-2])
 ip1s = twiss_df.s["ip1"]
 
@@ -104,7 +104,7 @@
 # Let's again retrieve the ``TWISS`` table, then plot the new conditions in the
 # Interaction Region.
 
-twiss_df_waist = madx.table.twiss.dframe().copy()
+twiss_df_waist = madx.table.twiss.dframe()
 twiss_df_waist.name = twiss_df.name.apply(lambda x: x[:-2])
 ip1s = twiss_df_waist.s["ip1"]
 
@@ -186,7 +186,7 @@
     lhc.make_lhc_thin(madx, sequence=f"lhcb1", slicefactor=4)
     lhc.add_markers_around_lhc_ip(madx, sequence=f"lhcb1", ip=1, n_markers=1000, interval=0.001)
     madx.command.twiss()
-    initial_twiss = madx.table.twiss.dframe().copy()
+    initial_twiss = madx.table.twiss.dframe()
 
     # Calling pre-calculated and re-matched waist shift knobs
     for knobfile in b1_knobs:
@@ -197,7 +197,7 @@
     matching.match_tunes_and_chromaticities(madx, "lhc", f"lhcb1", 62.31, 60.32, 2.0, 2.0)
 
     madx.command.twiss()
-    twiss_df = madx.table.twiss.dframe().copy()
+    twiss_df = madx.table.twiss.dframe()
 
 ###############################################################################
 # We will use all our added markers to determine the location of the waist,

pyhdtoolkit/cpymadtools/coupling.py

@@ -51,12 +51,6 @@ def get_closest_tune_approach(
         This assumes the sequence has previously been matched to the user's desired working point, as if not
         explicitely given, the appropriate targets will be determined from the ``MAD-X`` internal tables.
 
-    .. important::
-        This is hard-coded to use the ``CHROM`` flag when performing matching, since we expect to be in
-        the presence of betatron coupling. In this case, attempting to match chromaticities at the same time as the
-        tunes might cause ``LMDIF`` to fail, as the knobs become dependent. For this reason, only tune matching is
-        performed here, and chromaticities are voluntarily ignored.
-
     Args:
         madx (cpymad.madx.Madx): an instanciated `~cpymad.madx.Madx` object.
         accelerator (Optional[str]): name of the accelerator, used to determmine knobs if *variables* is not given.
@@ -99,7 +93,7 @@ def get_closest_tune_approach(
         tune_knobs, _ = lhc_knobs[:2], lhc_knobs[2:]  # first two for tune & last two for chroma, not used
 
     logger.debug("Running TWISS to update SUMM and TWISS tables")
-    madx.command.twiss(chrom=True)
+    madx.command.twiss()
 
     logger.debug("Saving knob values to restore after closest tune approach")
     varied_knobs = varied_knobs or tune_knobs  # if accelerator was given we've extracted this already
@@ -142,7 +136,7 @@ def get_closest_tune_approach(
     logger.debug("Restoring saved knobs")
     with madx.batch():
         madx.globals.update(saved_knobs)
-    madx.command.twiss(chrom=True)  # make sure TWISS and SUMM tables are returned to their original state
+    madx.command.twiss()  # make sure TWISS and SUMM tables are returned to their original state
 
     return cminus
 
@@ -206,7 +200,7 @@ def get_cminus_from_coupling_rdts(
             >>> complex_cminus = get_cminus_from_coupling_rdts(madx, patterns=["^BPM.*B[12]$"])
     """
     logger.debug(f"Getting coupling RDTs at selected elements thoughout the machine")
-    twiss_with_rdts = get_pattern_twiss(madx, patterns=patterns, columns=MONITOR_TWISS_COLUMNS, chrom=True)
+    twiss_with_rdts = get_pattern_twiss(madx, patterns=patterns, columns=MONITOR_TWISS_COLUMNS)
     twiss_with_rdts.columns = twiss_with_rdts.columns.str.upper()  # optics_functions needs capitalized names
     twiss_with_rdts[["F1001", "F1010"]] = coupling_via_cmatrix(twiss_with_rdts, output=["rdts"])
 
@@ -263,7 +257,7 @@ def match_no_coupling_through_ripkens(
     madx.input("do_ripken: macro = {twiss, ripken=True;}")  # cpymad needs .input for macros
 
     logger.debug("Matching Parameters")
-    madx.command.match(sequence=sequence, use_macro=True, chrom=True)
+    madx.command.match(sequence=sequence, use_macro=True)
     for knob in vary_knobs:
         madx.command.vary(name=knob)
     madx.command.use_macro(name="do_ripken")
@@ -283,7 +277,6 @@ def get_coupling_rdts(madx: Madx, **kwargs) -> tfs.TfsDataFrame:
     Args:
         madx (cpymad.madx.Madx): an instanciated `~cpymad.madx.Madx` object.
         **kwargs: any keyword argument will be transmitted to the ``TWISS`` command in ``MAD-X``.
-            Note that ``CHROM`` is already provided as it is needed for the RDTs' calculation.
 
     Returns:
         A `~tfs.TfsDataFrame` with columns of the ``TWISS`` table, and two complex columns for the
@@ -294,7 +287,7 @@ def get_coupling_rdts(madx: Madx, **kwargs) -> tfs.TfsDataFrame:
 
             >>> twiss_rdts = get_coupling_rdts(madx)
     """
-    twiss_tfs = get_twiss_tfs(madx, chrom=True, **kwargs)
+    twiss_tfs = get_twiss_tfs(madx, **kwargs)
     twiss_tfs[["F1001", "F1010"]] = coupling_via_cmatrix(twiss_tfs, output=["rdts"])
     return twiss_tfs
 

pyhdtoolkit/cpymadtools/lhc/_coupling.py

@@ -49,7 +49,7 @@ def correct_lhc_global_coupling(
 
     real_knob, imag_knob = f"CMRS.b{beam:d}{suffix}", f"CMIS.b{beam:d}{suffix}"
     logger.debug(f"Matching using the coupling knobs '{real_knob}' and '{imag_knob}'")
-    madx.command.match(chrom=True, sequence=sequence)
+    madx.command.match(sequence=sequence)
     madx.command.gweight(dqmin=1, Q1=0)
     madx.command.global_(dqmin=0, Q1=62.28)
     madx.command.vary(name=real_knob, step=1.0e-8)
@@ -77,9 +77,7 @@ def get_lhc_bpms_twiss_and_rdts(madx: Madx) -> tfs.TfsDataFrame:
 
             >>> twiss_with_rdts = get_lhc_bpms_twiss_and_rdts(madx)
     """
-    twiss_tfs = twiss.get_pattern_twiss(  # need chromatic flag as we're dealing with coupling
-        madx, patterns=["^BPM.*B[12]$"], columns=MONITOR_TWISS_COLUMNS, chrom=True
-    )
+    twiss_tfs = twiss.get_pattern_twiss(madx, patterns=["^BPM.*B[12]$"], columns=MONITOR_TWISS_COLUMNS)
     twiss_tfs.columns = twiss_tfs.columns.str.upper()  # optics_functions needs capitalized names
     twiss_tfs.NAME = twiss_tfs.NAME.str.upper()
     twiss_tfs[["F1001", "F1010"]] = coupling_via_cmatrix(twiss_tfs, output=["rdts"])

pyhdtoolkit/cpymadtools/lhc/_misc.py

@@ -197,6 +197,6 @@ def get_sizes_at_ip(madx: Madx, ip: int, geom_emit_x: float = None, geom_emit_y:
     geom_emit_x = geom_emit_x or madx.globals["geometric_emit_x"]
     geom_emit_y = geom_emit_y or madx.globals["geometric_emit_y"]
 
-    twiss_tfs = twiss.get_twiss_tfs(madx, chrom=True, ripken=True)
+    twiss_tfs = twiss.get_twiss_tfs(madx, ripken=True)
     twiss_tfs = _add_beam_size_to_df(twiss_tfs, geom_emit_x, geom_emit_y)
     return twiss_tfs.loc[f"IP{ip:d}"].SIZE_X, twiss_tfs.loc[f"IP{ip:d}"].SIZE_Y

pyhdtoolkit/cpymadtools/lhc/_routines.py

@@ -129,7 +129,7 @@ def correct_lhc_global_coupling(
 
     real_knob, imag_knob = f"CMRS.b{beam:d}{suffix}", f"CMIS.b{beam:d}{suffix}"
     logger.debug(f"Matching using the coupling knobs '{real_knob}' and '{imag_knob}'")
-    madx.command.match(chrom=True, sequence=sequence)
+    madx.command.match(sequence=sequence)
     madx.command.gweight(dqmin=1, Q1=0)
     madx.command.global_(dqmin=0, Q1=62.28)
     madx.command.vary(name=real_knob, step=1.0e-8)
@@ -181,6 +181,6 @@ def correct_lhc_orbit(
 
     for _ in range(iterations):
         logger.trace("Doing orbit correction for Y then X plane")
-        madx.twiss(chrom=True)
+        madx.command.twiss()
         madx.command.correct(sequence=sequence, plane="y", flag="ring", error=orbit_tolerance, mode=mode, **kwargs)
         madx.command.correct(sequence=sequence, plane="x", flag="ring", error=orbit_tolerance, mode=mode, **kwargs)

pyhdtoolkit/cpymadtools/matching.py

@@ -66,9 +66,6 @@ def match_tunes_and_chromaticities(
         If explicit knobs are provided, these will always be used. On other machines the knobs should be provided
         explicitly, always.
 
-    .. important::
-        The matching is always performed with the ``CHROM`` option on.
-
     Args:
         madx (cpymad.madx.Madx): an instanciated `~cpymad.madx.Madx` object.
         accelerator (Optional[str]): name of the accelerator, used to determmine knobs if *variables* is not given.
@@ -129,7 +126,7 @@ def match_tunes_and_chromaticities(
     def match(*args, **kwargs):
         """Create matching commands for kwarg targets, varying the given args."""
         logger.debug(f"Executing matching commands, using sequence '{sequence}'")
-        madx.command.match(chrom=True)
+        madx.command.match()
         logger.trace(f"Targets are given as {kwargs}")
         madx.command.global_(sequence=sequence, **kwargs)
         for variable_name in args:
@@ -138,7 +135,7 @@ def match(*args, **kwargs):
         madx.command.lmdif(calls=calls, tolerance=tolerance)
         madx.command.endmatch()
         logger.trace("Performing routine TWISS")
-        madx.twiss(chrom=True)  # prevents errors if the user forgets to TWISS before querying tables
+        madx.command.twiss()  # prevents errors if the user forgets to TWISS before querying tables
 
     # Case of a combined matching: both tune and chroma targets have been provided
     if q1_target is not None and q2_target is not None and dq1_target is not None and dq2_target is not None:
@@ -191,9 +188,6 @@ def match_tunes(
         This is a wrapper around the `~.match_tunes_and_chromaticities` function. Refer to its documentation
         for usage details.
 
-    .. important::
-        The matching is always performed with the ``CHROM`` option on.
-
     Args:
         madx (cpymad.madx.Madx): an instanciated `~cpymad.madx.Madx` object.
         accelerator (Optional[str]): name of the accelerator, used to determmine knobs if *variables* is not given.
@@ -275,9 +269,6 @@ def match_chromaticities(
         This is a wrapper around the `~.match_tunes_and_chromaticities` function. Refer to its documentation
         for usage details.
 
-    .. important::
-        The matching is always performed with the ``CHROM`` option on.
-
     Args:
         madx (cpymad.madx.Madx): an instanciated `~cpymad.madx.Madx` object.
         accelerator (Optional[str]): name of the accelerator, used to determmine knobs if *variables* is not given.

pyhdtoolkit/cpymadtools/ptc.py

@@ -333,9 +333,9 @@ def ptc_track_particle(
 
     if onetable:  # user asked for ONETABLE, there will only be one table 'trackone' given back by MAD-X
         logger.debug("Because of option ONETABLE only one table 'TRACKONE' exists to be returned.")
-        return {"trackone": madx.table.trackone.dframe().copy()}
+        return {"trackone": madx.table.trackone.dframe()}
     return {
-        f"observation_point_{point:d}": madx.table[f"track.obs{point:04d}.p0001"].dframe().copy()
+        f"observation_point_{point:d}": madx.table[f"track.obs{point:04d}.p0001"].dframe()
         for point in range(1, len(observation_points) + 2)  # len(observation_points) + 1 for start of
         # machine + 1 because MAD-X starts indexing these at 1
     }

pyhdtoolkit/cpymadtools/track.py

@@ -92,9 +92,9 @@ def track_single_particle(
     madx.command.endtrack()
     if onetable:  # user asked for ONETABLE, there will only be one table 'trackone' given back by MAD-X
         logger.debug("Because of option ONETABLE only one table 'TRACKONE' exists to be returned.")
-        return {"trackone": madx.table.trackone.dframe().copy()}
+        return {"trackone": madx.table.trackone.dframe()}
     return {
-        f"observation_point_{point:d}": madx.table[f"track.obs{point:04d}.p0001"].dframe().copy()
+        f"observation_point_{point:d}": madx.table[f"track.obs{point:04d}.p0001"].dframe()
         for point in range(1, len(observation_points) + 2)  # len(observation_points) + 1 for start of
         # machine + 1 because MAD-X starts indexing these at 1
     }

pyhdtoolkit/cpymadtools/twiss.py

@@ -86,7 +86,7 @@ def get_pattern_twiss(
     madx.twiss(**kwargs)
 
     logger.trace("Extracting relevant parts of the TWISS table")
-    twiss_df = tfs.TfsDataFrame(madx.table.twiss.dframe().copy())
+    twiss_df = tfs.TfsDataFrame(madx.table.twiss.dframe())
     twiss_df.headers = {var.upper(): madx.table.summ[var][0] for var in madx.table.summ}
     twiss_df = twiss_df[madx.table.twiss.selected_columns()].iloc[madx.table.twiss.selected_rows()]
 

pyhdtoolkit/optics/ripken.py

@@ -45,7 +45,7 @@ def lebedev_beam_size(
 
             >>> geom_emit_x = madx.globals["geometric_emit_x"]
             >>> geom_emit_y = madx.globals["geometric_emit_y"]
-            >>> twiss_tfs = madx.twiss(ripken=True).dframe().copy()
+            >>> twiss_tfs = madx.twiss(ripken=True).dframe()
             >>> horizontal_size = lebedev_beam_size(
                     twiss_tfs.beta11, twiss_tfs.beta21, geom_emit_x, geom_emit_y
                 )

pyhdtoolkit/plotting/aperture.py

@@ -98,7 +98,7 @@ def plot_aperture(
     logger.debug("Plotting aperture limits and machine layout")
     logger.debug("Getting Twiss dataframe from cpymad")
     madx.command.twiss(centre=True)
-    twiss_df: pd.DataFrame = madx.table.twiss.dframe().copy()
+    twiss_df: pd.DataFrame = madx.table.twiss.dframe()
     aperture_df = pd.DataFrame.from_dict(dict(madx.table.aperture))  # slicing -> issues with .dframe()
 
     # Restrict the span of twiss_df to avoid plotting all elements then cropping when xlimits is given

pyhdtoolkit/plotting/crossing.py

@@ -70,12 +70,12 @@ def plot_two_lhc_ips_crossings(
     logger.debug("Getting TWISS table for LHCB1")
     madx.use(sequence="lhcb1")
     madx.command.twiss(centre=True)
-    twiss_df_b1 = madx.table.twiss.dframe().copy()
+    twiss_df_b1 = madx.table.twiss.dframe()
 
     logger.debug("Getting TWISS table for LHCB2")
     madx.use(sequence="lhcb2")
     madx.command.twiss(centre=True)
-    twiss_df_b2 = madx.table.twiss.dframe().copy()
+    twiss_df_b2 = madx.table.twiss.dframe()
 
     logger.trace("Determining exact locations of IP points")
     first_ip_s = twiss_df_b1.s[f"ip{first_ip}"]

pyhdtoolkit/plotting/envelope.py

@@ -172,11 +172,11 @@ def _interpolate_madx(madx: Madx) -> None:
 def _get_twiss_hr_from_madx(madx: Madx, beam_params: BeamParameters) -> pd.DataFrame:
     """Get twiss hr from the provided MAD-X instance."""
     logger.trace("Getting Twiss dframe from MAD-X")
-    twiss_hr: pd.DataFrame = madx.table.twiss.dframe().copy()
+    twiss_hr: pd.DataFrame = madx.table.twiss.dframe()
     twiss_hr["betatronic_envelope_x"] = np.sqrt(twiss_hr.betx * beam_params.eg_x_m)
     twiss_hr["betatronic_envelope_y"] = np.sqrt(twiss_hr.bety * beam_params.eg_y_m)
     twiss_hr["dispersive_envelope_x"] = twiss_hr.dx * beam_params.deltap_p
     twiss_hr["dispersive_envelope_y"] = twiss_hr.dy * beam_params.deltap_p
-    twiss_hr["envelope_x"] = np.sqrt(twiss_hr.betatronic_envelope_x**2 + (twiss_hr.dx * beam_params.deltap_p) ** 2)
-    twiss_hr["envelope_y"] = np.sqrt(twiss_hr.betatronic_envelope_y**2 + (twiss_hr.dy * beam_params.deltap_p) ** 2)
+    twiss_hr["envelope_x"] = np.sqrt(twiss_hr.betatronic_envelope_x ** 2 + (twiss_hr.dx * beam_params.deltap_p) ** 2)
+    twiss_hr["envelope_y"] = np.sqrt(twiss_hr.betatronic_envelope_y ** 2 + (twiss_hr.dy * beam_params.deltap_p) ** 2)
     return twiss_hr

pyhdtoolkit/plotting/styles/paper.py

@@ -21,7 +21,7 @@
 SINGLE_COLUMN: Dict[str, PlotSetting] = {
     # ------ Lines ------ #
     "lines.linewidth": 1.3,  # Width of plot lines
-    "lines.markersize": 2,  # Marker size, in points
+    "lines.markersize": 5,  # Marker size, in points
     # ------ Patches ------ #
     "patch.linewidth": 1.2,  # Width of patches edge lines
     # ------ Fonts ------ #
@@ -54,7 +54,7 @@
     "legend.frameon": True,  # Make a dedicated patch for the legend
     "legend.framealpha": 0.85,  # Legend patch transparency factor
     "legend.fancybox": True,  # Use rounded box for legend background
-    "legend.fontsize": 24,  # Legend text font size
+    "legend.fontsize": 20,  # Legend text font size
     # ------ Figure ------ #
     "figure.figsize": (11, 7),  # Size of the figure
     "figure.titlesize": 20,  # Size of the figure title

pyhdtoolkit/plotting/utils.py

@@ -201,7 +201,7 @@ def make_survey_groups(madx: Madx) -> Dict[str, pd.DataFrame]:
     logger.debug("Getting different element groups dframes from MAD-X survey")
     madx.command.survey()
 
-    survey_df = madx.table.survey.dframe().copy()
+    survey_df = madx.table.survey.dframe()
     return {
         "dipoles": survey_df[survey_df.index.isin(element_dfs["dipoles"].index.tolist())],
         "quad_foc": survey_df[survey_df.index.isin(quadrupoles_focusing_df.index.tolist())],
@@ -356,7 +356,7 @@ def _get_twiss_table_with_offsets_and_limits(
     # Restrict the span of twiss_df to avoid plotting all elements then cropping when xlimits is given
     logger.trace("Getting TWISS table from MAD-X")
     madx.command.twiss()
-    twiss_df = madx.table.twiss.dframe().copy()
+    twiss_df = madx.table.twiss.dframe()
     twiss_df.s = twiss_df.s - xoffset
     twiss_df = twiss_df[twiss_df.s.between(*xlimits)] if xlimits else twiss_df
     return twiss_df

pyhdtoolkit/utils/_misc.py

@@ -86,7 +86,7 @@ def apply_colin_corrs_balance(madx: Madx) -> None:
     lhc.misalign_lhc_ir_quadrupoles(madx, ips=[8], beam=1, quadrupoles=[3], sides="R", DPSI=1e-3)
     madx.globals["kqsx3.l8"] = -5e-4
     madx.globals["kqsx3.r8"] = -5e-4
-    madx.command.twiss(chrom=True)
+    madx.command.twiss()
 
 
 # ----- Fetching Utilities ----- #