plothist 1.5.0__py3-none-any.whl → 1.6.0__py3-none-any.whl

plothist/__init__.py

@@ -85,18 +85,19 @@ __all__ = [
 ]
 
 
-# Get style file and use it
+from importlib import resources
 from importlib.resources import files
 
+import boost_histogram as bh
+import matplotlib.font_manager as fm
 import matplotlib.pyplot as plt
 
+# Get style file and use it
+
 style_file = files("plothist").joinpath("default_style.mplstyle")
 plt.style.use(style_file)
 
 # Install fonts
-from importlib import resources
-
-import matplotlib.font_manager as fm
 
 with resources.as_file(resources.files("plothist_utils") / "fonts") as font_path:
     font_files = fm.findSystemFonts(fontpaths=[str(font_path)])
@@ -104,7 +105,6 @@ with resources.as_file(resources.files("plothist_utils") / "fonts") as font_path
         fm.fontManager.addfont(font)
 
 # Check version of boost_histogram
-import boost_histogram as bh
 
 if tuple(int(part) for part in bh.__version__.split(".")) < (1, 4, 0):
     raise ImportError(

plothist/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.5.0'
-__version_tuple__ = version_tuple = (1, 5, 0)
+__version__ = version = '1.6.0'
+__version_tuple__ = version_tuple = (1, 6, 0)

plothist/comparison.py

@@ -22,9 +22,16 @@ def _check_uncertainty_type(uncertainty_type: str) -> None:
         If the uncertainty type is not valid.
 
     """
-    if uncertainty_type not in ["symmetrical", "asymmetrical"]:
+    _valid_uncertainty_types = [
+        "symmetrical",
+        "asymmetrical",
+        "asymmetrical_double_sided_zeros",
+        "asymmetrical_one_sided_zeros",
+    ]
+
+    if uncertainty_type not in _valid_uncertainty_types:
         raise ValueError(
-            f"Uncertainty type {uncertainty_type} not valid. Must be 'symmetrical' or 'asymmetrical'."
+            f"Uncertainty type {uncertainty_type} not valid. Must be in {_valid_uncertainty_types}."
         )
 
 
@@ -42,11 +49,12 @@ def _is_unweighted(hist: bh.Histogram) -> bool:
     bool
         True if the histogram is unweighted, False otherwise.
     """
-    return np.allclose(hist.variances(), hist.values())
+    return np.allclose(hist.variances(), hist.values(), equal_nan=True)
 
 
 def get_asymmetrical_uncertainties(
     hist: bh.Histogram,
+    uncertainty_type: str = "asymmetrical",
 ) -> tuple[np.ndarray, np.ndarray]:
     """
     Get Poisson asymmetrical uncertainties for a histogram via a frequentist approach based on a confidence-interval computation.
@@ -57,6 +65,8 @@ def get_asymmetrical_uncertainties(
     ----------
     hist : bh.Histogram
         The histogram.
+    uncertainty_type : str, optional
+        The type of uncertainty to compute for bins with 0 entry. Default is "asymmetrical" (= "asymmetrical_one_sided_zeros"). Use "asymmetrical_double_sided_zeros" to have the double-sided definition. More information in :ref:`documentation-statistics-label`.
 
     Returns
     -------
@@ -72,16 +82,44 @@ def get_asymmetrical_uncertainties(
 
     """
     _check_counting_histogram(hist)
+    _check_uncertainty_type(uncertainty_type)
 
     if not _is_unweighted(hist):
         raise ValueError(
             "Asymmetrical uncertainties can only be computed for an unweighted histogram."
         )
-    conf_level = 0.682689492
-    alpha = 1.0 - conf_level
+
+    alpha = 1.0 - 0.682689492
+    tail_probability = alpha / 2
+
     n = hist.values()
-    uncertainties_low = n - stats.gamma.ppf(alpha / 2, n, scale=1)
-    uncertainties_high = stats.gamma.ppf(1 - alpha / 2, n + 1, scale=1) - n
+
+    lower_bound = np.zeros_like(n, dtype=float)
+    upper_bound = np.zeros_like(n, dtype=float)
+
+    # Two-sided Garwood intervals for n > 0
+    lower_bound[n > 0] = stats.gamma.ppf(q=tail_probability, a=n[n > 0], scale=1)
+    upper_bound[n > 0] = stats.gamma.ppf(
+        q=1 - tail_probability, a=n[n > 0] + 1, scale=1
+    )
+
+    if uncertainty_type == "asymmetrical_double_sided_zeros":
+        # Two-sided Garwood intervals for n == 0
+        upper_bound[n == 0] = stats.gamma.ppf(q=1 - tail_probability, a=1, scale=1)
+    elif uncertainty_type in ["asymmetrical_one_sided_zeros", "asymmetrical"]:
+        # One-sided upper limit for n == 0
+        upper_bound[n == 0] = stats.gamma.ppf(q=1 - 2 * tail_probability, a=1, scale=1)
+    else:
+        raise ValueError(
+            f"Invalid uncertainty type '{uncertainty_type}' for asymmetrical uncertainties."
+        )
+
+    # Compute asymmetric uncertainties
+    uncertainties_low = n - lower_bound
+    uncertainties_high = upper_bound - n
+
+    uncertainties_low = np.nan_to_num(uncertainties_low, nan=0.0)
+    uncertainties_high = np.nan_to_num(uncertainties_high, nan=0.0)
 
     return uncertainties_low, uncertainties_high
 
@@ -174,8 +212,10 @@ def get_pull(
     _check_counting_histogram(h1)
     _check_counting_histogram(h2)
 
-    if h1_uncertainty_type == "asymmetrical":
-        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(h1)
+    if "asymmetrical" in h1_uncertainty_type:
+        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(
+            h1, h1_uncertainty_type
+        )
         h1_variances = np.where(
             h1.values() >= h2.values(),
             uncertainties_low**2,
@@ -232,8 +272,10 @@ def get_difference(
 
     difference_values = h1.values() - h2.values()
 
-    if h1_uncertainty_type == "asymmetrical":
-        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(h1)
+    if "asymmetrical" in h1_uncertainty_type:
+        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(
+            h1, h1_uncertainty_type
+        )
 
         difference_uncertainties_low = np.sqrt(uncertainties_low**2 + h2.variances())
         difference_uncertainties_high = np.sqrt(uncertainties_high**2 + h2.variances())
@@ -390,11 +432,13 @@ def get_ratio(
 
     ratio_values = np.where(h2.values() != 0, h1.values() / h2.values(), np.nan)
 
-    if h1_uncertainty_type == "asymmetrical":
-        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(h1)
+    if "asymmetrical" in h1_uncertainty_type:
+        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(
+            h1, h1_uncertainty_type
+        )
 
     if ratio_uncertainty_type == "uncorrelated":
-        if h1_uncertainty_type == "asymmetrical":
+        if "asymmetrical" in h1_uncertainty_type:
             h1_high = h1.copy()
             h1_high[:] = np.c_[h1_high.values(), uncertainties_high**2]
             h1_low = h1.copy()
@@ -405,7 +449,7 @@ def get_ratio(
             ratio_uncertainties_low = np.sqrt(get_ratio_variances(h1, h2))
             ratio_uncertainties_high = ratio_uncertainties_low
     elif ratio_uncertainty_type == "split":
-        if h1_uncertainty_type == "asymmetrical":
+        if "asymmetrical" in h1_uncertainty_type:
             ratio_uncertainties_low = uncertainties_low / h2.values()
             ratio_uncertainties_high = uncertainties_high / h2.values()
         else:
@@ -493,7 +537,7 @@ def get_comparison(
                 h1, h2, h1_uncertainty_type
             )
         elif comparison == "asymmetry":
-            if h1_uncertainty_type == "asymmetrical":
+            if "asymmetrical" in h1_uncertainty_type:
                 raise ValueError(
                     "Asymmetrical uncertainties are not supported for the asymmetry comparison."
                 )
@@ -501,7 +545,7 @@ def get_comparison(
             lower_uncertainties = uncertainties
             upper_uncertainties = uncertainties
         elif comparison == "efficiency":
-            if h1_uncertainty_type == "asymmetrical":
+            if "asymmetrical" in h1_uncertainty_type:
                 raise ValueError(
                     "Asymmetrical uncertainties are not supported in an efficiency computation."
                 )

plothist/examples/utility/uncertainty_types.py

@@ -0,0 +1,120 @@
+"""
+Representation of different uncertainty types.
+==============================================
+
+This example demonstrates how to use the `plot_error_hist` function with different uncertainty types
+"""
+
+import boost_histogram as bh
+import matplotlib.pyplot as plt
+import numpy as np
+
+from plothist import add_text, plot_error_hist
+
+
+def shifted_array(values, offset: int, size: int = 15) -> np.ndarray:
+    """
+    Create an array of a given size with NaNs and fill it with values at specified offsets.
+    The values are inserted at every offset starting from the given offset.
+    """
+
+    arr = np.full(size, np.nan)
+    indices = range(offset, size, len(values))
+
+    for i, idx in enumerate(indices):
+        if i >= len(values):
+            break
+        arr[idx] = values[i]
+
+    return arr
+
+
+def make_grouped_edges(
+    n_groups, group_size=4, inner_spacing=0.1, inter_spacing=0.2
+) -> np.ndarray:
+    """
+    Create a set of edges for a histogram with grouped categories.
+    """
+
+    edges = [
+        group_start + i * inner_spacing
+        for group in range(n_groups)
+        for i in range(group_size)
+        for group_start in [
+            group * (group_size * inner_spacing + inter_spacing - inner_spacing)
+        ]
+    ]
+    return np.array(edges)
+
+
+# Create a category axis with explicit locations
+edges = make_grouped_edges(4)
+axis = bh.axis.Variable(edges)
+
+hists = []
+entries = [0, 0.5, 3, 500]
+
+for k in range(3):
+    hist = bh.Histogram(axis, storage=bh.storage.Weight())
+    values = shifted_array(entries, k)
+    hist[:] = np.c_[values, values]
+    hists.append(hist)
+
+
+fig, (ax_top, ax_bot) = plt.subplots(
+    2, 1, gridspec_kw={"height_ratios": [1, 3], "hspace": 0.05}
+)
+
+for ax in (ax_top, ax_bot):
+    plot_error_hist(
+        hists[0], ax=ax, label="symmetrical", uncertainty_type="symmetrical"
+    )
+    plot_error_hist(
+        hists[1], ax=ax, label="asymmetrical", uncertainty_type="asymmetrical"
+    )
+    plot_error_hist(
+        hists[2],
+        ax=ax,
+        label="asymmetrical_double_sided_zeros",
+        uncertainty_type="asymmetrical_double_sided_zeros",
+    )
+
+add_text("plot_error_hist() with different uncertainty type", ax=ax_top, x="right")
+
+# Set axis limits
+ax_top.set_ylim(465, 530)
+ax_bot.set_ylim(-0.5, 6.9)
+ax_bot.set_xlim(xmin=-0.05)
+
+# Format bottom ticks and labels
+ax_bot.set_xticks(edges[1::4] + 0.05)
+ax_bot.set_xlabel("Entry category")
+ax_bot.set_xticklabels(entries)
+ax_bot.set_ylabel("Entries")
+ax_bot.yaxis.label.set_horizontalalignment("left")
+ax_bot.spines.top.set_visible(False)
+ax_bot.xaxis.set_minor_locator(plt.NullLocator())  # Hide x-axis minor ticks
+
+# Format top ticks and labels
+ax_top.xaxis.tick_top()
+ax_top.spines.bottom.set_visible(False)
+ax_top.set_xticklabels([])
+ax_top.set_xticks([])
+
+# Draw break marks
+d = 0.5  # proportion of vertical to horizontal extent of the slanted line
+kwargs = {
+    "marker": [(-1, -d), (1, d)],
+    "markersize": 12,
+    "linestyle": "none",
+    "color": "k",
+    "mec": "k",
+    "mew": 1,
+    "clip_on": False,
+}
+ax_top.plot([0, 1], [0, 0], transform=ax_top.transAxes, **kwargs)
+ax_bot.plot([0, 1], [1, 1], transform=ax_bot.transAxes, **kwargs)
+
+ax_top.legend(loc="upper left")
+
+fig.savefig("uncertainty_types.svg", bbox_inches="tight")

plothist/plothist_style.py

@@ -112,7 +112,7 @@ def cubehelix_palette(
     pal = cmap(x)[:, :3].tolist()
     if reverse:
         pal = pal[::-1]
-    return pal
+    return [tuple(c) for c in pal]
 
 
 def get_color_palette(
@@ -170,7 +170,7 @@ def get_color_palette(
         )
 
     plt_cmap = plt.get_cmap(cmap)
-    return plt_cmap(np.linspace(0, 1, N))
+    return [tuple(k) for k in plt_cmap(np.linspace(0, 1, N))]
 
 
 def set_fitting_ylabel_fontsize(ax: plt.Axes) -> float:

plothist/plotters.py

@@ -406,7 +406,9 @@ def plot_error_hist(
     if uncertainty_type == "symmetrical":
         kwargs.setdefault("yerr", np.sqrt(hist.variances()))
     else:
-        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(hist)
+        uncertainties_low, uncertainties_high = get_asymmetrical_uncertainties(
+            hist, uncertainty_type
+        )
         kwargs.setdefault("yerr", [uncertainties_low, uncertainties_high])
 
     kwargs.setdefault("fmt", ".")

{plothist-1.5.0.dist-info → plothist-1.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: plothist
-Version: 1.5.0
+Version: 1.6.0
 Summary: Plot histograms in a scalable way and a beautiful style.
 Project-URL: Homepage, https://github.com/cyrraz/plothist
 Project-URL: Documentation, https://plothist.readthedocs.io/

{plothist-1.5.0.dist-info → plothist-1.6.0.dist-info}/RECORD

@@ -1,11 +1,11 @@
-plothist/__init__.py,sha256=00yQZBIlyvZxdimTgPMHK_ZH5pNVadyi-fu6ezuXRQs,2760
-plothist/_version.py,sha256=qEW4HoWHYDkBguijNs9nZzHd38qlKSeRTDG2QQbYrGY,511
+plothist/__init__.py,sha256=ikcYOZqMs4WKAJ2rM-3BnHu_CQxLlQCuc-iFo_a-Mns,2760
+plothist/_version.py,sha256=5FGJNp9Lkk9uOxeCjXpoCGBF79Ar6LGPOR7-atBqb_4,511
 plothist/_version.pyi,sha256=o7uNL6MhuJoiqpEnriU7rBT6TmkJZA-i2qMoNz9YcgQ,82
-plothist/comparison.py,sha256=Lk5bTMHe93C_0eOfUJQaY8lHxykJIQBWMDDt-iOmR-E,17935
+plothist/comparison.py,sha256=jkONOiCp8RNBk8V_VvwACdfJJqo89rK9NQW71XxJscc,19623
 plothist/default_style.mplstyle,sha256=7MmB2uiXmD_DSqFHeH1xxC-lTctBD_EASxMdSOsPep0,1574
 plothist/histogramming.py,sha256=o0RLdoEhxHA7Ws0bvK3DewsbQEu-QOtJNw5Md5AckHM,11474
-plothist/plothist_style.py,sha256=oPGt61GT6Hs_m6jRNlNDGCH1-5AJuMMUi7guw1vTGVo,13215
-plothist/plotters.py,sha256=hjoDKVTYfRXI1m0GxlkfPc2LnpQWH1aYC8GnsYEak9k,46296
+plothist/plothist_style.py,sha256=bbYFc-qsrTfdbacCBAAzmiHJoRIh3toBomFfxtTRNMs,13255
+plothist/plotters.py,sha256=ncPZa34Fo1mbFxv0guFc2zEciX_JXGKJxeIfcUDaP6w,46336
 plothist/test_helpers.py,sha256=JXhxUdqMszkawxkU8cDPqipkSXNHfsKSfe3K-4frDrM,1379
 plothist/variable_registry.py,sha256=usVLoDLbIMzjeRDazIH0OIjQIUsh9RSJ9Ncnhn1V9qw,10783
 plothist/examples/README.rst,sha256=PVzkOQzVnNeWORxEv3NNv5XoSN2Y71D7SYzRkCqirfA,151
@@ -56,8 +56,9 @@ plothist/examples/utility/add_text_example.py,sha256=EB7ZUStt2E8GawjWNmVbSV34NIN
 plothist/examples/utility/color_palette_hists.py,sha256=uIc6TrmjTj8EUif1Yj1wq4nXoY1sgJpS15yPe3-FpTw,2383
 plothist/examples/utility/color_palette_squares.py,sha256=pNasgvZZApu-sCqhi5FTJAH3l6Px2cgB5RwJcQ1eF1U,2689
 plothist/examples/utility/matplotlib_vs_plothist_style.py,sha256=iEIfbFKmAN-PcDCzw_sBuhrfpes4I2wUVfC0r1vUHEw,2006
-plothist-1.5.0.dist-info/METADATA,sha256=0km7Qp4BxeY3aBXgC7EdkIShgSlNVo6yOnR6ehC16a0,4737
-plothist-1.5.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-plothist-1.5.0.dist-info/licenses/AUTHORS.md,sha256=02x3_8PNyTsXcRs0IlJeCTOmpGNRqymcJ71-2QtR37E,111
-plothist-1.5.0.dist-info/licenses/LICENSE,sha256=bfaEdGehofQDaw-zDdVMHNUKo1FrOm6oGUEF-ltrp6w,1523
-plothist-1.5.0.dist-info/RECORD,,
+plothist/examples/utility/uncertainty_types.py,sha256=r1yxzEvxn5Clv0ZIok9JjVh3RB-YQ_usWhFnpvl1els,3259
+plothist-1.6.0.dist-info/METADATA,sha256=WsoMGQrcmUasAx0UxEP9aGEw7LAk1eHQCrjUz6228fY,4737
+plothist-1.6.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+plothist-1.6.0.dist-info/licenses/AUTHORS.md,sha256=02x3_8PNyTsXcRs0IlJeCTOmpGNRqymcJ71-2QtR37E,111
+plothist-1.6.0.dist-info/licenses/LICENSE,sha256=bfaEdGehofQDaw-zDdVMHNUKo1FrOm6oGUEF-ltrp6w,1523
+plothist-1.6.0.dist-info/RECORD,,