diff --git a/.buildinfo b/.buildinfo index fae7dc0..107ca64 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 697e294e6b213e7a504d5c0aee1bc23a +config: 1f976f3864c3e25791bd2d9c988bcca4 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 8d048c5..83d955c 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -1,21 +1,23 @@ - + - Overview: module code — turn_by_turn 0.5.0 documentation - - - + Overview: module code — turn_by_turn 0.6.0 documentation + + + + + - - - - - + + + + + @@ -34,7 +36,7 @@
- 0.5 + 0.6
diff --git a/_modules/turn_by_turn/esrf.html b/_modules/turn_by_turn/esrf.html index 922bf40..8082783 100644 --- a/_modules/turn_by_turn/esrf.html +++ b/_modules/turn_by_turn/esrf.html @@ -1,21 +1,23 @@ - + - turn_by_turn.esrf — turn_by_turn 0.5.0 documentation - - - + turn_by_turn.esrf — turn_by_turn 0.6.0 documentation + + + + + - - - - - + + + + + @@ -34,7 +36,7 @@
- 0.5 + 0.6
@@ -142,7 +144,9 @@

Source code for turn_by_turn.esrf

 LOGGER = logging.getLogger()
 
 
-
[docs]def read_tbt(file_path: Union[str, Path]) -> TbtData:
+

+[docs]
+def read_tbt(file_path: Union[str, Path]) -> TbtData:
     """
     Reads turn-by-turn data from the ``ESRF``'s **Matlab** format file.
 
@@ -158,7 +162,10 @@ 
Source code for turn_by_turn.esrf
     return numpy_to_tbt(names, matrix)

 
 
-
[docs]def load_esrf_mat_file(infile: Union[str, Path]) -> Tuple[np.ndarray, np.ndarray]:
+
+

+[docs]
+def load_esrf_mat_file(infile: Union[str, Path]) -> Tuple[np.ndarray, np.ndarray]:
     """
     Reads the **ESRF** TbT ``Matlab`` file, checks for nans and matrices duplicities from consecutive kicks.
 
@@ -188,6 +195,7 @@ 
Source code for turn_by_turn.esrf
     return np.array(bpm_names), tbt_data

 
 
+
 def _check_esrf_tbt_data(tbt_data: np.ndarray) -> np.ndarray:
     tbt_data[np.isnan(np.sum(tbt_data, axis=3)), :] = 0.0
     # check if contains the same matrices as in previous kick
diff --git a/_modules/turn_by_turn/io.html b/_modules/turn_by_turn/io.html
index 9754dca..f9eb739 100644
--- a/_modules/turn_by_turn/io.html
+++ b/_modules/turn_by_turn/io.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.io — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.io — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -153,7 +155,9 @@ 
Source code for turn_by_turn.io
 write_lhc_ascii = write_ascii  # Backwards compatibility <0.4
 
 
-
[docs]def read_tbt(file_path: Union[str, Path], datatype: str = "lhc") -> TbtData:
+

+[docs]
+def read_tbt(file_path: Union[str, Path], datatype: str = "lhc") -> TbtData:
     """
     Calls the appropriate loader for the provided matrices type and returns a ``TbtData`` object of the
     loaded matrices.
@@ -179,7 +183,10 @@ 
Source code for turn_by_turn.io
         return module.read_tbt(file_path)

 
 
-
[docs]def write_tbt(output_path: Union[str, Path], tbt_data: TbtData, noise: float = None, seed: int = None, datatype: str = "lhc") -> None:
+
+

+[docs]
+def write_tbt(output_path: Union[str, Path], tbt_data: TbtData, noise: float = None, seed: int = None, datatype: str = "lhc") -> None:
     """
     Write a ``TbtData`` object's data to file, in the ``LHC``'s **SDDS** format.
 
@@ -211,6 +218,7 @@ 
Source code for turn_by_turn.io
         if noise is not None:
             tbt_data = add_noise_to_tbt(tbt_data, noise=noise, seed=seed)
         return module.write_tbt(output_path, tbt_data)

+
 

 
            

diff --git a/_modules/turn_by_turn/iota.html b/_modules/turn_by_turn/iota.html
index ec4904b..59dd4a3 100644
--- a/_modules/turn_by_turn/iota.html
+++ b/_modules/turn_by_turn/iota.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.iota — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.iota — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -147,7 +149,9 @@ 
Source code for turn_by_turn.iota
 }
 
 
-
[docs]def read_tbt(file_path: Union[str, Path], hdf5_version: int = 2) -> TbtData:
+

+[docs]
+def read_tbt(file_path: Union[str, Path], hdf5_version: int = 2) -> TbtData:
     """
     Reads turn-by-turn data from ``IOITA``'s **hdf5** format file.
     As there are 2 possible versions of the HDF5 format, this will try them both successively.
@@ -184,6 +188,7 @@ 
Source code for turn_by_turn.iota
     return TbtData(matrices=matrices, bunch_ids=bunch_ids, nturns=nturns)

 
 
+
 def _get_turn_by_turn_data_v1(hdf5_v1_file: h5py.File, plane: str, version: int) -> np.ndarray:
     """Go through the file to determine the turn-by-turn data as a numpy array, for an hdf5 v1 file."""
     keys = [key for key in hdf5_v1_file.keys() if (key.endswith(PLANES_CONV[version][plane]))]
diff --git a/_modules/turn_by_turn/lhc.html b/_modules/turn_by_turn/lhc.html
index aaa5f27..1cbfa4a 100644
--- a/_modules/turn_by_turn/lhc.html
+++ b/_modules/turn_by_turn/lhc.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.lhc — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.lhc — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -157,7 +159,9 @@ 
Source code for turn_by_turn.lhc
 }
 
 
-
[docs]def read_tbt(file_path: Union[str, Path]) -> TbtData:
+

+[docs]
+def read_tbt(file_path: Union[str, Path]) -> TbtData:
     """
     Reads turn-by-turn data from the ``LHC``'s **SDDS** format file.
     Will first determine if it is in ASCII format to figure out which reading method to use.
@@ -172,8 +176,7 @@ 
Source code for turn_by_turn.lhc
     LOGGER.debug(f"Reading LHC file at path: '{file_path.absolute()}'")
 
     if is_ascii_file(file_path):
-        matrices, date = read_ascii(file_path)
-        return TbtData(matrices, date, [0], matrices[0].X.shape[1])
+        return read_ascii(file_path)
 
     sdds_file = sdds.read(file_path)
     nbunches = sdds_file.values[N_BUNCHES]
@@ -204,7 +207,10 @@ 
Source code for turn_by_turn.lhc
     return TbtData(matrices, date, bunch_ids, nturns)

 
 
-
[docs]def write_tbt(output_path: Union[str, Path], tbt_data: TbtData) -> None:
+
+

+[docs]
+def write_tbt(output_path: Union[str, Path], tbt_data: TbtData) -> None:
     """
     Write a ``TbtData`` object's data to file, in the ``LHC``'s **SDDS** format.
 
@@ -236,6 +242,7 @@ 
Source code for turn_by_turn.lhc
         np.ravel(data[PLANE_TO_NUM["Y"]]),
         ]
     sdds.write(sdds.SddsFile("SDDS1", None, definitions, values), output_path)

+
 

 
            

diff --git a/_modules/turn_by_turn/ptc.html b/_modules/turn_by_turn/ptc.html
index 276fc7d..fb9fd41 100644
--- a/_modules/turn_by_turn/ptc.html
+++ b/_modules/turn_by_turn/ptc.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.ptc — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.ptc — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -162,7 +164,9 @@ 
Source code for turn_by_turn.ptc
 TIME_FORMAT: str = "%d/%m/%y %H.%M.%S"
 
 
-
[docs]def read_tbt(file_path: Union[str, Path]) -> TbtData:
+

+[docs]
+def read_tbt(file_path: Union[str, Path]) -> TbtData:
     """
     Reads turn-by-turn data from the ``PTC`` **trackone** format file.
 
@@ -196,6 +200,7 @@ 
Source code for turn_by_turn.ptc
     return TbtData(matrices=matrices, date=date, bunch_ids=particles, nturns=n_turns)

 
 
+
 def _read_header(lines: Sequence[str]) -> Tuple[datetime, int]:
     """Reads header length and datetime from header."""
     idx_line = 0
diff --git a/_modules/turn_by_turn/structures.html b/_modules/turn_by_turn/structures.html
index a9fc09b..fbd7964 100644
--- a/_modules/turn_by_turn/structures.html
+++ b/_modules/turn_by_turn/structures.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.structures — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.structures — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -133,7 +135,9 @@ 
Source code for turn_by_turn.structures
 from dateutil import tz
 
 
-
[docs]@dataclass
+

+[docs]
+@dataclass
 class TransverseData:
     """
     Object holding measured turn-by-turn data for both transverse planes in the form of pandas DataFrames.
@@ -142,18 +146,24 @@ 
Source code for turn_by_turn.structures
     X: pd.DataFrame  # horizontal data
     Y: pd.DataFrame  # vertical data
 
-
[docs]    @classmethod
+

+[docs]
+    @classmethod
     def fieldnames(self) -> List[str]:
         """Return a list of the fields of this dataclass."""
         return list(f.name for f in fields(self))

 
+
     def __getitem__(self, item):  # to access X and Y like one would with a dictionary
         if item not in self.fieldnames():
             raise KeyError(f"'{item}' is not in the fields of a {self.__class__.__name__} object.")
         return getattr(self, item)

 
 
-
[docs]@dataclass
+
+

+[docs]
+@dataclass
 class TrackingData:
     """
     Object holding multidimensional turn-by-turn simulation data in the form of pandas DataFrames.
@@ -168,21 +178,27 @@ 
Source code for turn_by_turn.structures
     S: pd.DataFrame  # longitudinal position data
     E: pd.DataFrame  # energy data
 
-
[docs]    @classmethod
+

+[docs]
+    @classmethod
     def fieldnames(self) -> List[str]:
         """Return a list of the fields of this dataclass."""
         return list(f.name for f in fields(self))

 
+
     def __getitem__(self, item):  # to access fields like one would with a dictionary
         if item not in self.fieldnames():
             raise KeyError(f"'{item}' is not in the fields of a {self.__class__.__name__} object.")
         return getattr(self, item)

 
 
+
 DataType = Union[TransverseData, TrackingData]
 
 
-
[docs]@dataclass
+

+[docs]
+@dataclass
 class TbtData:
     """
     Object holding a representation of a Turn-by-Turn data measurement. The date of the measurement,
@@ -208,6 +224,7 @@ 
Source code for turn_by_turn.structures
 
         if self.bunch_ids is None:
             self.bunch_ids = list(range(self.nbunches))  # we always need bunch-ids

+
 

 
            

diff --git a/_modules/turn_by_turn/trackone.html b/_modules/turn_by_turn/trackone.html
index de9e858..a2c6172 100644
--- a/_modules/turn_by_turn/trackone.html
+++ b/_modules/turn_by_turn/trackone.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.trackone — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.trackone — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -140,7 +142,9 @@ 
Source code for turn_by_turn.trackone
 LOGGER = logging.getLogger()
 
 
-
[docs]def read_tbt(file_path: Union[str, Path], is_tracking_data: bool = False) -> TbtData:
+

+[docs]
+def read_tbt(file_path: Union[str, Path], is_tracking_data: bool = False) -> TbtData:
     """
     Reads turn-by-turn data from the ``MAD-X`` **trackone** format file.
 
@@ -164,7 +168,10 @@ 
Source code for turn_by_turn.trackone
         return numpy_to_tbt(names, matrix[[0, 2]], datatype=TransverseData)

 
 
-
[docs]def get_trackone_stats(file_path: Union[str, Path], write_out: bool = False) -> Tuple[int, int]:
+
+

+[docs]
+def get_trackone_stats(file_path: Union[str, Path], write_out: bool = False) -> Tuple[int, int]:
     """
     Determines the number of particles and turns in the matrices from the provided ``MAD-X``
     **trackone** file.
@@ -205,7 +212,10 @@ 
Source code for turn_by_turn.trackone
     return nturns - 1, nparticles

 
 
-
[docs]def get_structure_from_trackone(
+
+

+[docs]
+def get_structure_from_trackone(
     nturns: int = 0, npart: int = 0, file_path: Union[str, Path] = "trackone"
 ) -> Tuple[np.ndarray, np.ndarray]:
     """
@@ -241,6 +251,7 @@ 
Source code for turn_by_turn.trackone
                     parts[2:]
                 )
     return np.array(list(bpms.keys())), np.transpose(np.array(list(bpms.values())), axes=[3, 0, 1, 2])

+
 

 
            

diff --git a/_modules/turn_by_turn/utils.html b/_modules/turn_by_turn/utils.html
index dbff6e6..e526a56 100644
--- a/_modules/turn_by_turn/utils.html
+++ b/_modules/turn_by_turn/utils.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  turn_by_turn.utils — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  turn_by_turn.utils — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -138,7 +140,9 @@ 
Source code for turn_by_turn.utils
 LOGGER = logging.getLogger(__name__)
 
 
-
[docs]def generate_average_tbtdata(tbtdata: TbtData) -> TbtData:
+

+[docs]
+def generate_average_tbtdata(tbtdata: TbtData) -> TbtData:
     """
     Takes a ``TbtData`` object and returns another containing the averaged matrices over all
     bunches/particles at all used BPMs.
@@ -168,7 +172,10 @@ 
Source code for turn_by_turn.utils
     return TbtData(new_matrices, tbtdata.date, [1], tbtdata.nturns)

 
 
-
[docs]def get_averaged_data(
+
+

+[docs]
+def get_averaged_data(
     bpm_names: Sequence[str], matrices: Sequence[TransverseData], plane: str, turns: int
 ) -> np.ndarray:
     """
@@ -193,7 +200,10 @@ 
Source code for turn_by_turn.utils
     return np.nanmean(bpm_data, axis=1)

 
 
-
[docs]def matrices_to_array(tbt_data: TbtData) -> np.ndarray:
+
+

+[docs]
+def matrices_to_array(tbt_data: TbtData) -> np.ndarray:
     """
     Convert  the matrices of a ``TbtData`` object to a numpy array.
 
@@ -214,7 +224,10 @@ 
Source code for turn_by_turn.utils
     return data

 
 
-
[docs]def add_noise(data: np.ndarray, noise: float = None, sigma: float = None, seed: int = None) -> np.ndarray:
+
+

+[docs]
+def add_noise(data: np.ndarray, noise: float = None, sigma: float = None, seed: int = None) -> np.ndarray:
     """
     Returns the given data with added noise. Noise is generated as a standard normal distribution (mean=0,
     standard_deviation=1) with the size of the input data, and scaled by the a factor before being added to
@@ -242,7 +255,10 @@ 
Source code for turn_by_turn.utils
     return np.array(data + scaling * np.random.default_rng(seed).standard_normal(data.shape))

 
 
-
[docs]def add_noise_to_tbt(data: TbtData, noise: float = None, sigma: float = None, seed: int = None) -> TbtData:
+
+

+[docs]
+def add_noise_to_tbt(data: TbtData, noise: float = None, sigma: float = None, seed: int = None) -> TbtData:
     """
     Returns a new copy of the given TbT data with added noise.
     The noise is generated by :func:`turn_by_turn.utils.add_noise` from a single rng,
@@ -270,7 +286,10 @@ 
Source code for turn_by_turn.utils
     )

 
 
-
[docs]def numpy_to_tbt(names: np.ndarray, matrix: np.ndarray, datatype: DataType = TransverseData) -> TbtData:
+
+

+[docs]
+def numpy_to_tbt(names: np.ndarray, matrix: np.ndarray, datatype: DataType = TransverseData) -> TbtData:
     """
     Converts turn by turn matrices and names into a ``TbTData`` object.
 
@@ -301,6 +320,7 @@ 
Source code for turn_by_turn.utils
         )
         indices.append(idx_bunch)
     return TbtData(matrices=matrices, bunch_ids=indices, nturns=nturns)

+
 

 
            

diff --git a/_static/basic.css b/_static/basic.css
index 7577acb..30fee9d 100644
--- a/_static/basic.css
+++ b/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {
diff --git a/_static/css/theme.css b/_static/css/theme.css
index c03c88f..19a446a 100644
--- a/_static/css/theme.css
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@@ -1,4 +1,4 @@
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diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index 05374cd..3fc4608 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,6 +1,5 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.5.0',
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '0.6.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/_static/pygments.css b/_static/pygments.css
index 691aeb8..0d49244 100644
--- a/_static/pygments.css
+++ b/_static/pygments.css
@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #FF0000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #00A000 } /* Generic.Inserted */
diff --git a/_static/searchtools.js b/_static/searchtools.js
index 97d56a7..7918c3f 100644
--- a/_static/searchtools.js
+++ b/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**
diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js
index aae669d..8a96c69 100644
--- a/_static/sphinx_highlight.js
+++ b/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});
diff --git a/environment.pickle b/environment.pickle
index ba50e00..e238e20 100644
Binary files a/environment.pickle and b/environment.pickle differ
diff --git a/genindex.html b/genindex.html
index 9dfb01a..55b303a 100644
--- a/genindex.html
+++ b/genindex.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  Index — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  Index — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
      
@@ -34,7 +36,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
diff --git a/index.doctree b/index.doctree
index 04faf9c..40dc1f0 100644
Binary files a/index.doctree and b/index.doctree differ
diff --git a/index.html b/index.html
index b2810d7..2f83991 100644
--- a/index.html
+++ b/index.html
@@ -1,22 +1,24 @@
 
-
+
 
-  
+  
 
   
-  Welcome to turn_by_turn’ documentation! — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  Welcome to turn_by_turn’ documentation! — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
     
@@ -36,7 +38,7 @@
               
           
               

-                0.5
+                0.6
               

 

   
@@ -122,12 +124,12 @@
            

              
   

-
Welcome to turn_by_turn’ documentation!

+
Welcome to turn_by_turn’ documentation!

 
turn_by_turn is a library for reading and writing from various particle accelerator measurement data formats used at CERN.

 
It provides a custom dataclass TbtData to do so, with attributes corresponding to the relevant measurements information.

 

 

-
Package Reference

+
Package Reference

 

 
Modules

 
    
@@ -170,7 +172,7 @@ 
    Package Reference
-
    Indices and tables
    
+
    Indices and tables
    
 
      
 
    • Index
      • 
 
    • Module Index
      • 
diff --git a/modules/index.doctree b/modules/index.doctree
index ece33a0..4020649 100644
Binary files a/modules/index.doctree and b/modules/index.doctree differ
diff --git a/modules/index.html b/modules/index.html
index d8eb47d..52be7a7 100644
--- a/modules/index.html
+++ b/modules/index.html
@@ -1,22 +1,24 @@
 
-
+
 
-  
+  
 
   
-  Constants — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  Constants — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
     
@@ -37,7 +39,7 @@
               
           
               
      
-                0.5
+                0.6
               
      
 
      
   
@@ -122,19 +124,19 @@
           
      
            
      
              
-  
      
-
      Constants
      
+  
      
+
      Constants
      
 
      Specific constants to be used in turn_by_turn, to help with consistency.
      
 
      
-
      
-
      IO
      
+
      
+
      IO
      
 
      This module contains high-level I/O functions to read and write tur-by-turn data objects in different
 formats. While data can be loaded from the formats of different machines / codes, each format getting its
 own reader module, writing functionality is at the moment always done in the LHC’s SDDS format.
      
 
      
 
      
 
      
-turn_by_turn.io.read_tbt(file_path: str | Path, datatype: str = 'lhc') → TbtData[source]
      
+turn_by_turn.io.read_tbt(file_path: str | Path, datatype: str = 'lhc') → TbtData[source]
 
      Calls the appropriate loader for the provided matrices type and returns a TbtData object of the
 loaded matrices.
      
 
      
@@ -153,7 +155,7 @@ 
      IO
 
 
      
 
      
-turn_by_turn.io.write_tbt(output_path: str | Path, tbt_data: TbtData, noise: float | None = None, seed: int | None = None, datatype: str = 'lhc') → None[source]
      
+turn_by_turn.io.write_tbt(output_path: str | Path, tbt_data: TbtData, noise: float | None = None, seed: int | None = None, datatype: str = 'lhc') → None[source]
 
      Write a TbtData object’s data to file, in the LHC’s SDDS format.
      
 
      
 
      Parameters:
      
@@ -171,24 +173,24 @@ 
      IO
 
      
 
      
 
-
      
-
      Structures
      
+
      
+
      Structures
      
 
      Data structures to be used in turn_by_turn to store turn-by-turn measurement data.
      
 
      
 
      
 
      
-class turn_by_turn.structures.TbtData(matrices: Sequence[TransverseData | TrackingData], date: datetime | None = None, bunch_ids: List[int] | None = None, nturns: int | None = None)[source]
      
+class turn_by_turn.structures.TbtData(matrices: Sequence[TransverseData | TrackingData], date: datetime | None = None, bunch_ids: List[int] | None = None, nturns: int | None = None)[source]
 
      Object holding a representation of a Turn-by-Turn data measurement. The date of the measurement,
 the transverse data, number of turns and bunches as well as the bunch IDs are encapsulated in this object.
      
 
      
 
 
      
 
      
-class turn_by_turn.structures.TrackingData(X: DataFrame, PX: DataFrame, Y: DataFrame, PY: DataFrame, T: DataFrame, PT: DataFrame, S: DataFrame, E: DataFrame)[source]
      
+class turn_by_turn.structures.TrackingData(X: DataFrame, PX: DataFrame, Y: DataFrame, PY: DataFrame, T: DataFrame, PT: DataFrame, S: DataFrame, E: DataFrame)[source]
 
      Object holding multidimensional turn-by-turn simulation data in the form of pandas DataFrames.
      
 
      
 
      
-classmethod fieldnames() → List[str][source]
      
+classmethod fieldnames() → List[str][source]
 
      Return a list of the fields of this dataclass.
      
 
      
 
@@ -196,23 +198,23 @@ 
      Structures
 
      
-class turn_by_turn.structures.TransverseData(X: DataFrame, Y: DataFrame)[source]
      
+class turn_by_turn.structures.TransverseData(X: DataFrame, Y: DataFrame)[source]
 
      Object holding measured turn-by-turn data for both transverse planes in the form of pandas DataFrames.
      
 
      
 
      
-classmethod fieldnames() → List[str][source]
      
+classmethod fieldnames() → List[str][source]
 
      Return a list of the fields of this dataclass.
      
 
      
 
 
      
 
-
      
-
      Utils
      
+
      
+
      Utils
      
 
      Utility functions for convenience operations on turn-by-turn data objects in this package.
      
 
      
 
      
 
      
-turn_by_turn.utils.add_noise(data: ndarray, noise: float | None = None, sigma: float | None = None, seed: int | None = None) → ndarray[source]
      
+turn_by_turn.utils.add_noise(data: ndarray, noise: float | None = None, sigma: float | None = None, seed: int | None = None) → ndarray[source]
 
      Returns the given data with added noise. Noise is generated as a standard normal distribution (mean=0,
 standard_deviation=1) with the size of the input data, and scaled by the a factor before being added to
 the provided data. Said factor can either be provided, or calculated from the input data’s own standard
@@ -235,7 +237,7 @@ 
      Utils
 
 
      
 
      
-turn_by_turn.utils.add_noise_to_tbt(data: TbtData, noise: float | None = None, sigma: float | None = None, seed: int | None = None) → TbtData[source]
      
+turn_by_turn.utils.add_noise_to_tbt(data: TbtData, noise: float | None = None, sigma: float | None = None, seed: int | None = None) → TbtData[source]
 
      Returns a new copy of the given TbT data with added noise.
 The noise is generated by turn_by_turn.utils.add_noise() from a single rng,
 i.e. the noise is not repeated on each dataframe.
      
@@ -257,7 +259,7 @@ 
      Utils
 
 
      
 
      
-turn_by_turn.utils.generate_average_tbtdata(tbtdata: TbtData) → TbtData[source]
      
+turn_by_turn.utils.generate_average_tbtdata(tbtdata: TbtData) → TbtData[source]
 
      Takes a TbtData object and returns another containing the averaged matrices over all
 bunches/particles at all used BPMs.
      
 
      
@@ -272,7 +274,7 @@ 
      Utils
 
 
      
 
      
-turn_by_turn.utils.get_averaged_data(bpm_names: Sequence[str], matrices: Sequence[TransverseData], plane: str, turns: int) → ndarray[source]
      
+turn_by_turn.utils.get_averaged_data(bpm_names: Sequence[str], matrices: Sequence[TransverseData], plane: str, turns: int) → ndarray[source]
 
      Average data from a given plane from the matrices of a TbtData.
      
 
      
 
      Parameters:
      
@@ -291,7 +293,7 @@ 
      Utils
 
 
      
 
      
-turn_by_turn.utils.matrices_to_array(tbt_data: TbtData) → ndarray[source]
      
+turn_by_turn.utils.matrices_to_array(tbt_data: TbtData) → ndarray[source]
 
      Convert  the matrices of a TbtData object to a numpy array.
      
 
      
 
      Parameters:
      
@@ -305,7 +307,7 @@ 
      Utils
 
 
      
 
      
-turn_by_turn.utils.numpy_to_tbt(names: ~numpy.ndarray, matrix: ~numpy.ndarray, datatype: ~turn_by_turn.structures.TransverseData | ~turn_by_turn.structures.TrackingData = <class 'turn_by_turn.structures.TransverseData'>) → TbtData[source]
      
+turn_by_turn.utils.numpy_to_tbt(names: ~numpy.ndarray, matrix: ~numpy.ndarray, datatype: ~turn_by_turn.structures.TransverseData | ~turn_by_turn.structures.TrackingData = <class 'turn_by_turn.structures.TransverseData'>) → TbtData[source]
 
      Converts turn by turn matrices and names into a TbTData object.
      
 
      
 
      Parameters:
      
diff --git a/objects.inv b/objects.inv
index d7af2cd..7a2e47f 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/py-modindex.html b/py-modindex.html
index 37dd44f..62b9930 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -1,21 +1,23 @@
 
-
+
 
   
   
-  Python Module Index — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  Python Module Index — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
     
@@ -37,7 +39,7 @@
               
           
               
      
-                0.5
+                0.6
               
      
 
      
   
diff --git a/readers/index.doctree b/readers/index.doctree
index 3c303f6..338f6f9 100644
Binary files a/readers/index.doctree and b/readers/index.doctree differ
diff --git a/readers/index.html b/readers/index.html
index a141998..036814d 100644
--- a/readers/index.html
+++ b/readers/index.html
@@ -1,22 +1,24 @@
 
-
+
 
-  
+  
 
   
-  ESRF — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  ESRF — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
   
   
-        
-        
-        
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+        
+        
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+        
     
     
     
@@ -36,7 +38,7 @@
               
           
               
      
-                0.5
+                0.6
               
      
 
      
   
@@ -121,14 +123,14 @@
           
      
            
      
              
-  
      
-
      ESRF
      
+  
      
+
      ESRF
      
 
      Data handling for turn-by-turn measurement files from ESRF (files in matlab format).
 This module is untested and should be considered experimental at the moment.
      
 
      
 
      
 
      
-turn_by_turn.esrf.load_esrf_mat_file(infile: str | Path) → Tuple[ndarray, ndarray][source]
      
+turn_by_turn.esrf.load_esrf_mat_file(infile: str | Path) → Tuple[ndarray, ndarray][source]
 
      Reads the ESRF TbT Matlab file, checks for nans and matrices duplicities from consecutive kicks.
      
 
      
 
      Parameters:
      
@@ -143,7 +145,7 @@ 
      ESRF
      
 
      
-turn_by_turn.esrf.read_tbt(file_path: str | Path) → TbtData[source]
      
+turn_by_turn.esrf.read_tbt(file_path: str | Path) → TbtData[source]
 
      Reads turn-by-turn data from the ESRF’s Matlab format file.
      
 
      
 
      Parameters:
      
@@ -155,13 +157,13 @@ 
      ESRF
      
 
      
 
-
      
-
      Iota
      
+
      
+
      Iota
      
 
      Data handling for turn-by-turn measurement files from Iota (files in hdf5 format).
      
 
      
 
      
 
      
-turn_by_turn.iota.read_tbt(file_path: str | Path, hdf5_version: int = 2) → TbtData[source]
      
+turn_by_turn.iota.read_tbt(file_path: str | Path, hdf5_version: int = 2) → TbtData[source]
 
      Reads turn-by-turn data from IOITA’s hdf5 format file.
 As there are 2 possible versions of the HDF5 format, this will try them both successively.
      
 
      
@@ -178,13 +180,13 @@ 
      Iota
      
 
      
 
-
      
-
      LHC
      
+
      
+
      LHC
      
 
      Data handling for turn-by-turn measurement files from the LHC (files in SDDS format).
      
 
      
 
      
 
      
-turn_by_turn.lhc.read_tbt(file_path: str | Path) → TbtData[source]
      
+turn_by_turn.lhc.read_tbt(file_path: str | Path) → TbtData[source]
 
      Reads turn-by-turn data from the LHC’s SDDS format file.
 Will first determine if it is in ASCII format to figure out which reading method to use.
      
 
      
@@ -199,7 +201,7 @@ 
      LHC
 
      
-turn_by_turn.lhc.write_tbt(output_path: str | Path, tbt_data: TbtData) → None[source]
      
+turn_by_turn.lhc.write_tbt(output_path: str | Path, tbt_data: TbtData) → None[source]
 
      Write a TbtData object’s data to file, in the LHC’s SDDS format.
      
 
      
 
      Parameters:
      
@@ -211,8 +213,8 @@ 
      LHC
 
      
 
-
      
-
      PTC
      
+
      
+
      PTC
      
 
      Data handling for turn-by-turn measurement files from the PTC code, which can be obtained by performing
 particle tracking of your machine through the MAD-X PTC interface. The files are very close in
 structure to TFS files, with the difference that the data part is split into “segments” relating
@@ -220,34 +222,34 @@ 
      PTC
 
      
 
      
-class turn_by_turn.ptc.Segment(number, turns, particles, element, name)
      
+class turn_by_turn.ptc.Segment(number, turns, particles, element, name)
 
      
 
      
-element
      
+element
 
      Alias for field number 3
      
 
      
 
 
      
 
      
-name
      
+name
 
      Alias for field number 4
      
 
      
 
 
      
 
      
-number
      
+number
 
      Alias for field number 0
      
 
      
 
 
      
 
      
-particles
      
+particles
 
      Alias for field number 2
      
 
      
 
 
      
 
      
-turns
      
+turns
 
      Alias for field number 1
      
 
      
 
@@ -255,7 +257,7 @@ 
      PTC
 
      
-turn_by_turn.ptc.read_tbt(file_path: str | Path) → TbtData[source]
      
+turn_by_turn.ptc.read_tbt(file_path: str | Path) → TbtData[source]
 
      Reads turn-by-turn data from the PTC trackone format file.
      
 
      
 
      Parameters:
      
@@ -267,8 +269,8 @@ 
      PTC
 
      
 
-
      
-
      Trackone
      
+
      
+
      Trackone
      
 
      Data handling for turn-by-turn measurement files from the MAD-X code, which can be obtained by performing
 particle tracking of your machine through in MAD-X. The files are very close in structure to TFS
 files, with the difference that the data part is split into “segments” relating containing data for a given
@@ -276,7 +278,7 @@ 
      Trackone
 
      
-turn_by_turn.trackone.get_structure_from_trackone(nturns: int = 0, npart: int = 0, file_path: str | Path = 'trackone') → Tuple[ndarray, ndarray][source]
      
+turn_by_turn.trackone.get_structure_from_trackone(nturns: int = 0, npart: int = 0, file_path: str | Path = 'trackone') → Tuple[ndarray, ndarray][source]
 
      Extracts BPM names and particle coordinates in the trackone file produced by MAD-X.
      
 
      
 
      Parameters:
      
@@ -297,7 +299,7 @@ 
      Trackone
 
      
-turn_by_turn.trackone.get_trackone_stats(file_path: str | Path, write_out: bool = False) → Tuple[int, int][source]
      
+turn_by_turn.trackone.get_trackone_stats(file_path: str | Path, write_out: bool = False) → Tuple[int, int][source]
 
      Determines the number of particles and turns in the matrices from the provided MAD-X
 trackone file.
      
 
      
@@ -315,7 +317,7 @@ 
      Trackone
 
      
-turn_by_turn.trackone.read_tbt(file_path: str | Path, is_tracking_data: bool = False) → TbtData[source]
      
+turn_by_turn.trackone.read_tbt(file_path: str | Path, is_tracking_data: bool = False) → TbtData[source]
 
      Reads turn-by-turn data from the MAD-X trackone format file.
      
 
      
 
      Parameters:
      
diff --git a/search.html b/search.html
index aa0cfe8..185212f 100644
--- a/search.html
+++ b/search.html
@@ -1,22 +1,24 @@
 
-
+
 
   
   
-  Search — turn_by_turn 0.5.0 documentation
-      
-      
-      
+  Search — turn_by_turn 0.6.0 documentation
+      
+      
+      
+
+  
     
   
   
-        
-        
-        
-        
-        
+        
+        
+        
+        
+        
     
     
     
@@ -37,7 +39,7 @@
               
           
               
      
-                0.5
+                0.6
               
      
 
      
   
diff --git a/searchindex.js b/searchindex.js
index 8e64cb3..86fd523 100644
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+++ b/searchindex.js
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\ No newline at end of file
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\ No newline at end of file