Merge pull request #51 from timmahrt/praatio_v6.1

Praatio 6.1
timmahrt · Nov 4, 2023 · 5ff7c78 · 5ff7c78
2 parents 0f0544e + 0f219e6
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diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,9 @@
 
 *Praatio uses semantic versioning (Major.Minor.Patch)*
 
+Ver 6.1 (Nov 4, 2023)
+- Add `TextgridTier.dejitter()` method for improving consistency between tiers
+
 Ver 6.0 (Feb 4, 2023)
 - Refactored 'audio.py' for maintainability (see [UPGRADING.md](https://github.com/timmahrt/praatIO/blob/main/UPGRADING.md) for details)
 - Added unit tests for 'audio.py'

diff --git a/README.md b/README.md
@@ -60,9 +60,7 @@ Please view [CHANGELOG.md](https://github.com/timmahrt/praatIO/blob/main/CHANGEL
 
 Python module `https://pypi.org/project/typing-extensions/`.  It should be installed automatically with praatio but you can install it manually if you have any problems.
 
-``Python 3.7.*`` or above
-
-[Click here to visit travis-ci and see the specific versions of python that praatIO is currently tested under](<https://travis-ci.org/timmahrt/praatIO>)
+``Python 3.7.*`` or above (CI tested with python `3.7` through `3.12`).
 
 If you are using ``Python 2.x`` or ``Python < 3.7``, you can use `PraatIO 4.x`.
 

diff --git a/docs/praatio.html b/docs/praatio.html
diff --git a/docs/praatio/audio.html b/docs/praatio/audio.html
diff --git a/docs/praatio/data_classes.html b/docs/praatio/data_classes.html
diff --git a/docs/praatio/data_classes/data_point.html b/docs/praatio/data_classes/data_point.html
diff --git a/docs/praatio/data_classes/interval_tier.html b/docs/praatio/data_classes/interval_tier.html
diff --git a/docs/praatio/data_classes/klattgrid.html b/docs/praatio/data_classes/klattgrid.html
diff --git a/docs/praatio/data_classes/point_tier.html b/docs/praatio/data_classes/point_tier.html
diff --git a/docs/praatio/data_classes/textgrid.html b/docs/praatio/data_classes/textgrid.html
diff --git a/docs/praatio/data_classes/textgrid_tier.html b/docs/praatio/data_classes/textgrid_tier.html
diff --git a/docs/praatio/data_points.html b/docs/praatio/data_points.html
diff --git a/docs/praatio/klattgrid.html b/docs/praatio/klattgrid.html
diff --git a/docs/praatio/pitch_and_intensity.html b/docs/praatio/pitch_and_intensity.html
diff --git a/docs/praatio/praat_scripts.html b/docs/praatio/praat_scripts.html
diff --git a/docs/praatio/praatio_scripts.html b/docs/praatio/praatio_scripts.html
diff --git a/docs/praatio/textgrid.html b/docs/praatio/textgrid.html
diff --git a/docs/praatio/utilities.html b/docs/praatio/utilities.html
diff --git a/docs/praatio/utilities/constants.html b/docs/praatio/utilities/constants.html
diff --git a/docs/praatio/utilities/errors.html b/docs/praatio/utilities/errors.html
diff --git a/docs/praatio/utilities/my_math.html b/docs/praatio/utilities/my_math.html
diff --git a/docs/praatio/utilities/textgrid_io.html b/docs/praatio/utilities/textgrid_io.html
diff --git a/docs/praatio/utilities/timit.html b/docs/praatio/utilities/timit.html
diff --git a/docs/praatio/utilities/utils.html b/docs/praatio/utilities/utils.html
diff --git a/docs/search.js b/docs/search.js
diff --git a/examples/get_pitch_and_formants.py b/examples/get_pitch_and_formants.py
@@ -74,7 +74,7 @@
     450,
     forceRegenerate=False,
 )
-tg = textgrid.openTextgrid(join(tgPath, "mary.TextGrid"))
+tg = textgrid.openTextgrid(join(tgPath, "mary.TextGrid"), False)
 tier = tg.getTier("phone")
 filteredData = tier.getValuesInIntervals(maryPitchData)
 

diff --git a/praatio/data_classes/interval_tier.py b/praatio/data_classes/interval_tier.py
@@ -14,6 +14,7 @@
 
 from praatio.utilities import errors
 from praatio.utilities import utils
+from praatio.utilities import my_math
 from praatio.utilities import constants
 
 from praatio.data_classes import textgrid_tier
@@ -100,6 +101,23 @@ def _validate(self):
                     f"({nextEntry.start}, {nextEntry.end}, {nextEntry.label})"
                 )
 
+    @property
+    def timestamps(self) -> List[float]:
+        """All unique timestamps used in this tier"""
+        tmpTimestamps = [
+            time
+            for start, stop, _ in self.entries
+            for time in [
+                start,
+                stop,
+            ]
+        ]
+
+        uniqueTimestamps = list(set(tmpTimestamps))
+        uniqueTimestamps.sort()
+
+        return uniqueTimestamps
+
     def crop(
         self,
         cropStart: float,
@@ -156,6 +174,42 @@ def crop(
 
         return croppedTier
 
+    def dejitter(
+        self,
+        referenceTier: textgrid_tier.TextgridTier,
+        maxDifference: float = 0.001,
+    ) -> textgrid_tier.TextgridTier:
+        """
+        Set timestamps in this tier to be the same as values in the reference tier
+
+        Timestamps will only be moved if they are less than maxDifference away from the
+        reference time.
+
+        This can be used to correct minor alignment errors between tiers, as made when
+        annotating files manually, etc.
+
+        Args:
+            referenceTier: the IntervalTier or PointTier to use as a reference
+            maxDifference: the maximum amount to allow timestamps to be moved by
+
+        Returns:
+            the modified version of the current tier
+        """
+        referenceTimestamps = referenceTier.timestamps
+
+        newEntries = []
+        for start, stop, label in self.entries:
+            startCompare = min(referenceTimestamps, key=lambda x: abs(x - start))
+            stopCompare = min(referenceTimestamps, key=lambda x: abs(x - stop))
+
+            if my_math.lessThanOrEqual(abs(start - startCompare), maxDifference):
+                start = startCompare
+            if my_math.lessThanOrEqual(abs(stop - stopCompare), maxDifference):
+                stop = stopCompare
+            newEntries.append((start, stop, label))
+
+        return self.new(entries=newEntries)
+
     def deleteEntry(self, entry: Interval) -> None:
         """Removes an entry from the entries"""
         self._entries.pop(self._entries.index(entry))

diff --git a/praatio/data_classes/klattgrid.py b/praatio/data_classes/klattgrid.py
@@ -138,6 +138,9 @@ def __init__(
     def crop(self):
         raise NotImplementedError
 
+    def dejitter(self):
+        raise NotImplementedError
+
     def deleteEntry(self, entry):
         raise NotImplementedError
 
@@ -153,6 +156,10 @@ def insertEntry(self):
     def insertSpace(self):
         raise NotImplementedError
 
+    @property
+    def timestamps(self):
+        raise NotImplementedError
+
     def validate(self):
         raise NotImplementedError
 
@@ -161,7 +168,7 @@ def modifyValues(self, modFunc: Callable[[float], bool]) -> None:
             (timestamp, modFunc(float(value))) for timestamp, value in self.entries
         ]
 
-        self.entries = newEntries
+        self._entries = newEntries
 
     def getAsText(self) -> str:
         outputList = []

diff --git a/praatio/data_classes/point_tier.py b/praatio/data_classes/point_tier.py
@@ -12,6 +12,7 @@
 from praatio.utilities import constants
 from praatio.utilities import errors
 from praatio.utilities import utils
+from praatio.utilities import my_math
 
 from praatio.data_classes import textgrid_tier
 
@@ -72,6 +73,16 @@ def __init__(
 
         super(PointTier, self).__init__(name, entries, calculatedMinT, calculatedMaxT)
 
+    @property
+    def timestamps(self) -> List[float]:
+        """All unique timestamps used in this tier"""
+        tmpTimestamps = [time for time, _ in self.entries]
+
+        uniqueTimestamps = list(set(tmpTimestamps))
+        uniqueTimestamps.sort()
+
+        return uniqueTimestamps
+
     def crop(
         self,
         cropStart: float,
@@ -121,6 +132,37 @@ def deleteEntry(self, entry: Point) -> None:
         """Removes an entry from the entries"""
         self._entries.pop(self._entries.index(entry))
 
+    def dejitter(
+        self, referenceTier: textgrid_tier.TextgridTier, maxDifference: float = 0.001
+    ) -> "PointTier":
+        """
+        Set timestamps in this tier to be the same as values in the reference tier
+
+        Timestamps will only be moved if they are less than maxDifference away from the
+        reference time.
+
+        This can be used to correct minor alignment errors between tiers, as made when
+        annotating files manually, etc.
+
+        Args:
+            referenceTier: the IntervalTier or PointTier to use as a reference
+            maxDifference: the maximum amount to allow timestamps to be moved by
+
+        Returns:
+            the modified version of the current tier
+        """
+        referenceTimestamps = referenceTier.timestamps
+
+        newEntries = []
+        for time, label in self.entries:
+            timeCompare = min(referenceTimestamps, key=lambda x: abs(x - time))
+
+            if my_math.lessThanOrEqual(abs(time - timeCompare), maxDifference):
+                time = timeCompare
+            newEntries.append((time, label))
+
+        return self.new(entries=newEntries)
+
     def editTimestamps(
         self,
         offset: float,

diff --git a/praatio/data_classes/textgrid_tier.py b/praatio/data_classes/textgrid_tier.py
@@ -75,6 +75,11 @@ def __eq__(self, other):
     def entries(self):
         return tuple(self._entries)
 
+    @property
+    @abstractmethod
+    def timestamps(self) -> List[float]:
+        pass
+
     def appendTier(self, tier: "TextgridTier") -> "TextgridTier":
         """Append a tier to the end of this one.
 
@@ -209,6 +214,14 @@ def insertEntry(
     ) -> None:  # pragma: no cover
         pass
 
+    @abstractmethod
+    def dejitter(
+        self,
+        referenceTier: "TextgridTier",
+        maxDifference: float = 0.001,
+    ) -> "TextgridTier":  # pragma: no cover
+        pass
+
     @abstractmethod
     def eraseRegion(
         self,

diff --git a/praatio/praatio_scripts.py b/praatio/praatio_scripts.py
@@ -434,6 +434,8 @@ def getValue(myBool) -> Literal["strict", "lax", "truncated"]:
     return outputFNList
 
 
+# TODO: Remove this method in the next major version
+#       Migrate to using the new Textgridtier.dejitter()
 def alignBoundariesAcrossTiers(
     tg: textgrid.Textgrid, tierName: str, maxDifference: float = 0.005
 ) -> textgrid.Textgrid:
@@ -464,7 +466,7 @@ def alignBoundariesAcrossTiers(
                        In such a case, choose a smaller maxDifference.
     """
     referenceTier = tg.getTier(tierName)
-    times = _getTimestampsFromTier(referenceTier)
+    times = referenceTier.timestamps
 
     for time, nextTime in zip(times[1::], times[2::]):
         if nextTime - time < maxDifference:
@@ -480,47 +482,7 @@ def alignBoundariesAcrossTiers(
         if tier.name == tierName:
             continue
 
-        newEntries: list = []
-        if tier.entryType == constants.Interval:
-            for start, stop, label in tier.entries:
-                startCompare = min(times, key=lambda x: abs(x - start))
-                stopCompare = min(times, key=lambda x: abs(x - stop))
-
-                if abs(start - startCompare) <= maxDifference:
-                    start = startCompare
-                if abs(stop - stopCompare) <= maxDifference:
-                    stop = stopCompare
-                newEntries.append((start, stop, label))
-        elif tier.entryType == constants.Point:
-            for time, label in tier.entries:
-                timeCompare = min(times, key=lambda x: abs(x - time))
-
-                if abs(time - timeCompare) <= maxDifference:
-                    time = timeCompare
-                newEntries.append((time, label))
-
-        tier = tier.new(entries=newEntries)
+        tier = tier.dejitter(referenceTier, maxDifference)
         tg.replaceTier(tier.name, tier)
 
     return tg
-
-
-def _getTimestampsFromTier(tier: textgrid_tier.TextgridTier) -> List[float]:
-    """Get all timestamps used in a tier"""
-    timestamps = []
-    if tier.entryType == constants.Interval:
-        timestamps = [
-            time
-            for start, stop, _ in tier.entries
-            for time in [
-                start,
-                stop,
-            ]
-        ]
-    elif tier.entryType == constants.Point:
-        timestamps = [time for time, _ in tier.entries]
-
-    timestamps = list(set(timestamps))
-    timestamps.sort()
-
-    return timestamps
diff --git a/praatio/utilities/my_math.py b/praatio/utilities/my_math.py
@@ -21,6 +21,10 @@ def isclose(a: float, b: float, rel_tol: float = 1e-14, abs_tol: float = 0.0) ->
     return abs(a - b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
 
 
+def lessThanOrEqual(a: float, b: float):
+    return isclose(a, b) or a < b
+
+
 def filterTimeSeriesData(
     filterFunc: Callable[[List[float], int, bool], List[float]],
     featureTimeList: List[list],

diff --git a/praatio/utilities/utils.py b/praatio/utilities/utils.py
@@ -6,7 +6,7 @@
 import subprocess
 import itertools
 import wave
-from pkg_resources import resource_filename
+from importlib import resources
 from typing_extensions import Literal
 from typing import Any, Iterator, List, Tuple, NoReturn, Type, Optional
 
@@ -15,11 +15,13 @@
 
 Interval = constants.Interval
 
-# Get the folder one level above the current folder
-scriptsPath = resource_filename(
-    "praatio",
-    "praatScripts",
-)
+# New in python 3.9
+if hasattr(resources, "files"):
+    scriptsPath = resources.files("praatio") / "praatScripts"
+# Deprecated in python 3.11
+else:
+    with resources.path("praatio", "praatScripts") as path:
+        scriptsPath = path
 
 
 def find(list, value, reverse) -> Optional[int]:
@@ -386,7 +388,6 @@ def findAll(txt: str, subStr: str) -> List[int]:
 def runPraatScript(
     praatEXE: str, scriptFN: str, argList: List[Any], cwd: str = None
 ) -> None:
-
     # Popen gives a not-very-transparent error
     if not os.path.exists(praatEXE):
         raise errors.FileNotFound(praatEXE)

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 setup(
     name="praatio",
     python_requires=">3.6.0",
-    version="6.0.1",
+    version="6.1.0",
     author="Tim Mahrt",
     author_email="timmahrt@gmail.com",
     url="https://github.com/timmahrt/praatIO",