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Improve UIntHistogram #54

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merged 2 commits into from
Oct 13, 2023
Merged

Improve UIntHistogram #54

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5691b30
Improve UIntHistogram
imagejan Oct 12, 2023
f5b323a
Add more tests
imagejan Oct 13, 2023
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Binary file added resources/legacy_hist.npz
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66 changes: 34 additions & 32 deletions src/faim_hcs/UIntHistogram.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@
"""
if data is not None:
assert data.min() >= 0, "Negative data is not supported."
self.offset, self.bins, self.frequencies = self._get_hist(data)
self.offset, _, self.frequencies = self._get_hist(data)
else:
self.offset, self.bins, self.frequencies = None, None, None
self.offset, self.frequencies = None, None

@staticmethod
def _add(list_a, list_b):
Expand All @@ -34,8 +34,8 @@
:return: offset, bins, frequencies
"""
offset = int(data.min())
bins = int(data.max()) + 2 - offset
freq = np.histogram(data, np.arange(offset, offset + bins))[0].tolist()
bins = int(data.max()) + 1 - offset
freq = np.histogram(data, np.arange(offset, offset + bins + 1))[0].tolist()
return offset, bins, freq

def _aggregate_histograms(self, offset_data, bins, freq):
Expand All @@ -52,7 +52,7 @@
"frequencies must be of " "type List."
)
lower_shift = offset_data - self.offset
upper_shift = self.offset + self.bins - (offset_data + bins)
upper_shift = self.offset + self.n_bins() + 1 - (offset_data + bins + 1)

if lower_shift == 0 and upper_shift == 0:
# Old and new frequencies cover the same range:
Expand All @@ -61,57 +61,53 @@
self.frequencies = self._add(self.frequencies, freq)
elif (
lower_shift < 0
and (offset_data + bins - 1 >= self.offset)
and (offset_data + bins - 1 <= self.offset + self.bins - 1)
and (offset_data + bins >= self.offset)
and (offset_data + bins <= self.offset + self.n_bins())
):
# New frequencies have additional lower ones.
# [old frequencies]
# [new frequencies]
frequencies_to = offset_data + bins - self.offset - 1
frequencies_to = offset_data + bins - self.offset
freq_from = self.offset - offset_data
self.frequencies[:frequencies_to] = self._add(
self.frequencies[:frequencies_to],
freq[freq_from:],
)
self.frequencies = freq[:freq_from] + self.frequencies
self.offset = offset_data
self.bins = len(self.frequencies) + 1
elif lower_shift < 0 and (offset_data + bins - 1 < self.offset):
elif lower_shift < 0 and (offset_data + bins < self.offset):
# New frequencies only have additional lower ones.
# [old frequencies]
# [new frequencies]
gap_freq = [
0,
] * (self.offset - offset_data - bins + 1)
] * (self.offset - offset_data - bins)
self.frequencies = freq + gap_freq + self.frequencies
self.offset = offset_data
self.bins = len(self.frequencies) + 1
elif (
self.offset
<= offset_data
<= (self.offset + self.bins - 2)
< offset_data + bins - 2
<= (self.offset + self.n_bins() - 1)
< offset_data + bins - 1
):
# New frequencies have additional upper ones.
# [old frequencies]
# [new frequencies]
from_frequencies = self.offset + self.bins - offset_data - 1
to_freq = self.offset + self.bins - offset_data
from_frequencies = self.offset + self.n_bins() - offset_data
to_freq = self.offset + self.n_bins() + 1 - offset_data
self.frequencies[-from_frequencies:] = self._add(
self.frequencies[-from_frequencies:],
freq[:to_freq],
)
self.frequencies = self.frequencies + freq[from_frequencies:]
self.bins = len(self.frequencies) + 1
elif (offset_data) > (self.offset + self.bins - 2):
elif (offset_data) > (self.offset + self.n_bins() - 1):
# New frequencies have only additional upper ones.
# [old frequencies]
# [new frequencies]
gap_freq = [
0,
] * (offset_data - self.offset - self.bins + 1)
] * (offset_data - self.offset - self.n_bins())
self.frequencies = self.frequencies + gap_freq + freq
self.bins = len(self.frequencies) + 1
elif lower_shift >= 0 and upper_shift >= 0:
# New frequencies are completely covered.
# [ old frequencies ]
Expand All @@ -129,14 +125,13 @@
# [old frequencies]
# [ new frequencies ]
from_ = self.offset - offset_data
to = from_ + self.bins - 1
to = from_ + self.n_bins()
self.frequencies = self._add(
self.frequencies,
freq[from_:to],
)
self.frequencies = freq[:from_] + self.frequencies + freq[to:]
self.offset = offset_data
self.bins = len(self.frequencies) + 1

def combine(self, histogram):
"""
Expand All @@ -146,13 +141,12 @@
"""
if self.frequencies is None:
self.frequencies = histogram.frequencies
self.bins = histogram.bins
self.offset = histogram.offset
else:
if histogram.frequencies is not None:
self._aggregate_histograms(
offset_data=histogram.offset,
bins=histogram.bins,
bins=histogram.n_bins(),
freq=histogram.frequencies,
)

Expand All @@ -168,7 +162,7 @@
assert data.min() >= 0, "Negative data is not supported."

if self.frequencies is None:
self.offset, self.bins, self.frequencies = self._get_hist(data)
self.offset, _, self.frequencies = self._get_hist(data)
else:
offset_data, bins, freq = self._get_hist(data)
self._aggregate_histograms(offset_data=offset_data, bins=bins, freq=freq)
Expand All @@ -181,13 +175,13 @@
"""
if width > 1:
heights = []
for i in range(self.offset, self.offset + self.bins - 1, width):
for i in range(self.offset, self.offset + self.n_bins(), width):

Check warning on line 178 in src/faim_hcs/UIntHistogram.py

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src/faim_hcs/UIntHistogram.py#L178 

Added line #L178 was not covered by tests
heights.append(np.sum(self.frequencies[i : i + width]))
else:
heights = self.frequencies

plt.bar(
np.arange(self.offset, self.offset + self.bins - 1, width),
np.arange(self.offset, self.offset + self.n_bins(), width),
heights,
width=width,
)
Expand All @@ -201,7 +195,7 @@
if self.frequencies is None:
return 0
return np.sum(
np.arange(self.offset, self.offset + self.bins - 1) * self.frequencies
np.arange(self.offset, self.offset + self.n_bins()) * self.frequencies
) / np.sum(self.frequencies)

def std(self):
Expand All @@ -213,7 +207,7 @@
return 0
return np.sqrt(
np.sum(
(np.arange(self.offset, self.offset + self.bins - 1) - self.mean()) ** 2
(np.arange(self.offset, self.offset + self.n_bins()) - self.mean()) ** 2
* self.frequencies
)
/ np.sum(self.frequencies)
Expand Down Expand Up @@ -248,16 +242,24 @@
"""
if self.frequencies is None:
return 0
return self.offset + self.bins - 2
return self.offset + self.n_bins() - 1

def n_bins(self):
"""Return number of bins.

:return: uint
"""
if self.frequencies is None:
return None
return len(self.frequencies)

def save(self, path):
np.savez(path, frequencies=self.frequencies, offset=self.offset, bins=self.bins)
np.savez(path, frequencies=self.frequencies, offset=self.offset)

@staticmethod
def load(path):
storage = np.load(path, allow_pickle=True)
hist = UIntHistogram()
hist.frequencies = storage["frequencies"].tolist()
hist.offset = storage["offset"]
hist.bins = storage["bins"]
return hist
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