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nyalldawsonnyalldawson
committedDec 1, 2016
[FEATURE][processing] New universal 'basic stats for field' algorithm
Replaces the existing 'Basic Stats for Numeric Fields' and 'Basic Stats for String Fields' algorithms and adds support for date/time/datetime fields. Having a single unified algorithm allows more flexible models where a field type may not be known in advance. Deprecate existing basic stats algorithms
·
ltr-3_40final-3_0_0
1 parent 1ff165a commit b30a1ff

13 files changed

+383
-11
lines changed
 

‎python/plugins/processing/algs/help/qgis.yaml

Lines changed: 3 additions & 7 deletions
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@@ -22,14 +22,10 @@ qgis:advancedpythonfieldcalculator: >
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qgis:barplot:
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qgis:basicstatisticsforfields: >
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This algorithm generates basic statistics from the analysis of a values in a field in the attribute table of a vector layer. Numeric, date, time and string fields are supported.
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qgis:basicstatisticsfornumericfields: >
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This algorithm generates basic statistics from the analysis of a numeric field in the attribute table of a vector layer.
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Statistics are generated as an HTML file.
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qgis:basicstatisticsfortextfields: >
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This algorithm generates basic statistics from the analysis of a text field in the attribute table of a vector layer.
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The statistics returned will depend on the field type.
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Statistics are generated as an HTML file.
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‎python/plugins/processing/algs/qgis/BasicStatistics.py

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@@ -0,0 +1,251 @@
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# -*- coding: utf-8 -*-
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"""
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***************************************************************************
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BasicStatistics.py
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---------------------
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Date : November 2016
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Copyright : (C) 2016 by Nyall Dawson
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Email : nyall dot dawson at gmail dot com
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***************************************************************************
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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***************************************************************************
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"""
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__author__ = 'Nyall Dawson'
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__date__ = 'November 2016'
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__copyright__ = '(C) 2016, Nyall Dawson'
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# This will get replaced with a git SHA1 when you do a git archive
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__revision__ = '$Format:%H$'
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import os
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import codecs
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from qgis.PyQt.QtCore import QVariant
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from qgis.PyQt.QtGui import QIcon
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from qgis.core import (QgsStatisticalSummary,
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QgsStringStatisticalSummary,
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QgsDateTimeStatisticalSummary,
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QgsFeatureRequest)
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from processing.core.GeoAlgorithm import GeoAlgorithm
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from processing.core.parameters import ParameterTable
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from processing.core.parameters import ParameterTableField
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from processing.core.outputs import OutputHTML
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from processing.core.outputs import OutputNumber
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from processing.tools import dataobjects, vector
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pluginPath = os.path.split(os.path.split(os.path.dirname(__file__))[0])[0]
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class BasicStatisticsForField(GeoAlgorithm):
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INPUT_LAYER = 'INPUT_LAYER'
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FIELD_NAME = 'FIELD_NAME'
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OUTPUT_HTML_FILE = 'OUTPUT_HTML_FILE'
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MIN = 'MIN'
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MAX = 'MAX'
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COUNT = 'COUNT'
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UNIQUE = 'UNIQUE'
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EMPTY = 'EMPTY'
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FILLED = 'FILLED'
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MIN_LENGTH = 'MIN_LENGTH'
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MAX_LENGTH = 'MAX_LENGTH'
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MEAN_LENGTH = 'MEAN_LENGTH'
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CV = 'CV'
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SUM = 'SUM'
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MEAN = 'MEAN'
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STD_DEV = 'STD_DEV'
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RANGE = 'RANGE'
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MEDIAN = 'MEDIAN'
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MINORITY = 'MINORITY'
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MAJORITY = 'MAJORITY'
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FIRSTQUARTILE = 'FIRSTQUARTILE'
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THIRDQUARTILE = 'THIRDQUARTILE'
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IQR = 'IQR'
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def getIcon(self):
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return QIcon(os.path.join(pluginPath, 'images', 'ftools', 'basic_statistics.png'))
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def defineCharacteristics(self):
81+
self.name, self.i18n_name = self.trAlgorithm('Basic statistics for fields')
82+
self.group, self.i18n_group = self.trAlgorithm('Vector table tools')
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self.tags = self.tr('stats,statistics,date,time,datetime,string,number,text,table,layer,maximum,minimum,mean,average,standard,deviation,'
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'count,distinct,unique,variance,median,quartile,range,majority,minority')
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self.addParameter(ParameterTable(self.INPUT_LAYER,
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self.tr('Input table')))
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self.addParameter(ParameterTableField(self.FIELD_NAME,
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self.tr('Field to calculate statistics on'),
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self.INPUT_LAYER))
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self.addOutput(OutputHTML(self.OUTPUT_HTML_FILE,
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self.tr('Statistics')))
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self.addOutput(OutputNumber(self.COUNT, self.tr('Count')))
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self.addOutput(OutputNumber(self.UNIQUE, self.tr('Number of unique values')))
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self.addOutput(OutputNumber(self.EMPTY, self.tr('Number of empty (null) values')))
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self.addOutput(OutputNumber(self.FILLED, self.tr('Number of non-empty values')))
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self.addOutput(OutputNumber(self.MIN, self.tr('Minimum value')))
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self.addOutput(OutputNumber(self.MAX, self.tr('Maximum value')))
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self.addOutput(OutputNumber(self.MIN_LENGTH, self.tr('Minimum length')))
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self.addOutput(OutputNumber(self.MAX_LENGTH, self.tr('Maximum length')))
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self.addOutput(OutputNumber(self.MEAN_LENGTH, self.tr('Mean length')))
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self.addOutput(OutputNumber(self.CV, self.tr('Coefficient of Variation')))
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self.addOutput(OutputNumber(self.SUM, self.tr('Sum')))
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self.addOutput(OutputNumber(self.MEAN, self.tr('Mean value')))
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self.addOutput(OutputNumber(self.STD_DEV, self.tr('Standard deviation')))
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self.addOutput(OutputNumber(self.RANGE, self.tr('Range')))
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self.addOutput(OutputNumber(self.MEDIAN, self.tr('Median')))
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self.addOutput(OutputNumber(self.MINORITY, self.tr('Minority (rarest occurring value)')))
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self.addOutput(OutputNumber(self.MAJORITY, self.tr('Majority (most frequently occurring value)')))
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self.addOutput(OutputNumber(self.FIRSTQUARTILE, self.tr('First quartile')))
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self.addOutput(OutputNumber(self.THIRDQUARTILE, self.tr('Third quartile')))
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self.addOutput(OutputNumber(self.IQR, self.tr('Interquartile Range (IQR)')))
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def processAlgorithm(self, progress):
117+
layer = dataobjects.getObjectFromUri(
118+
self.getParameterValue(self.INPUT_LAYER))
119+
field_name = self.getParameterValue(self.FIELD_NAME)
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field = layer.fields().at(layer.fields().lookupField(field_name))
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output_file = self.getOutputValue(self.OUTPUT_HTML_FILE)
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request = QgsFeatureRequest().setFlags(QgsFeatureRequest.NoGeometry).setSubsetOfAttributes([field_name], layer.fields())
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features = vector.features(layer, request)
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data = []
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data.append(self.tr('Analyzed layer: {}').format(layer.name()))
129+
data.append(self.tr('Analyzed field: {}').format(field_name))
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if field.isNumeric():
132+
data.extend(self.calcNumericStats(features, progress, field))
133+
elif field.type() in (QVariant.Date, QVariant.Time, QVariant.DateTime):
134+
data.extend(self.calcDateTimeStats(features, progress, field))
135+
else:
136+
data.extend(self.calcStringStats(features, progress, field))
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self.createHTML(output_file, data)
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def calcNumericStats(self, features, progress, field):
141+
count = len(features)
142+
total = 100.0 / float(count)
143+
stat = QgsStatisticalSummary()
144+
for current, ft in enumerate(features):
145+
stat.addVariant(ft[field.name()])
146+
progress.setPercentage(int(current * total))
147+
stat.finalize()
148+
149+
cv = stat.stDev() / stat.mean() if stat.mean() != 0 else 0
150+
151+
self.setOutputValue(self.COUNT, stat.count())
152+
self.setOutputValue(self.UNIQUE, stat.variety())
153+
self.setOutputValue(self.EMPTY, stat.countMissing())
154+
self.setOutputValue(self.FILLED, count - stat.countMissing())
155+
self.setOutputValue(self.MIN, stat.min())
156+
self.setOutputValue(self.MAX, stat.max())
157+
self.setOutputValue(self.RANGE, stat.range())
158+
self.setOutputValue(self.SUM, stat.sum())
159+
self.setOutputValue(self.MEAN, stat.mean())
160+
self.setOutputValue(self.MEDIAN, stat.median())
161+
self.setOutputValue(self.STD_DEV, stat.stDev())
162+
self.setOutputValue(self.CV, cv)
163+
self.setOutputValue(self.MINORITY, stat.minority())
164+
self.setOutputValue(self.MAJORITY, stat.majority())
165+
self.setOutputValue(self.FIRSTQUARTILE, stat.firstQuartile())
166+
self.setOutputValue(self.THIRDQUARTILE, stat.thirdQuartile())
167+
self.setOutputValue(self.IQR, stat.interQuartileRange())
168+
169+
data = []
170+
data.append(self.tr('Count: {}').format(stat.count()))
171+
data.append(self.tr('Unique values: {}').format(stat.variety()))
172+
data.append(self.tr('NULL (missing) values: {}').format(stat.countMissing()))
173+
data.append(self.tr('Minimum value: {}').format(stat.min()))
174+
data.append(self.tr('Maximum value: {}').format(stat.max()))
175+
data.append(self.tr('Range: {}').format(stat.range()))
176+
data.append(self.tr('Sum: {}').format(stat.sum()))
177+
data.append(self.tr('Mean value: {}').format(stat.mean()))
178+
data.append(self.tr('Median value: {}').format(stat.median()))
179+
data.append(self.tr('Standard deviation: {}').format(stat.stDev()))
180+
data.append(self.tr('Coefficient of Variation: {}').format(cv))
181+
data.append(self.tr('Minority (rarest occurring value): {}').format(stat.minority()))
182+
data.append(self.tr('Majority (most frequently occurring value): {}').format(stat.majority()))
183+
data.append(self.tr('First quartile: {}').format(stat.firstQuartile()))
184+
data.append(self.tr('Third quartile: {}').format(stat.thirdQuartile()))
185+
data.append(self.tr('Interquartile Range (IQR): {}').format(stat.interQuartileRange()))
186+
return data
187+
188+
def calcStringStats(self, features, progress, field):
189+
count = len(features)
190+
total = 100.0 / float(count)
191+
stat = QgsStringStatisticalSummary()
192+
for current, ft in enumerate(features):
193+
stat.addValue(ft[field.name()])
194+
progress.setPercentage(int(current * total))
195+
stat.finalize()
196+
197+
self.setOutputValue(self.COUNT, stat.count())
198+
self.setOutputValue(self.UNIQUE, stat.countDistinct())
199+
self.setOutputValue(self.EMPTY, stat.countMissing())
200+
self.setOutputValue(self.FILLED, stat.count() - stat.countMissing())
201+
self.setOutputValue(self.MIN, stat.min())
202+
self.setOutputValue(self.MAX, stat.max())
203+
self.setOutputValue(self.MIN_LENGTH, stat.minLength())
204+
self.setOutputValue(self.MAX_LENGTH, stat.maxLength())
205+
self.setOutputValue(self.MEAN_LENGTH, stat.meanLength())
206+
207+
data = []
208+
data.append(self.tr('Count: {}').format(count))
209+
data.append(self.tr('Unique values: {}').format(stat.countDistinct()))
210+
data.append(self.tr('NULL (missing) values: {}').format(stat.countMissing()))
211+
data.append(self.tr('Minimum value: {}').format(stat.min()))
212+
data.append(self.tr('Maximum value: {}').format(stat.max()))
213+
data.append(self.tr('Minimum length: {}').format(stat.minLength()))
214+
data.append(self.tr('Maximum length: {}').format(stat.maxLength()))
215+
data.append(self.tr('Mean length: {}').format(stat.meanLength()))
216+
217+
return data
218+
219+
def calcDateTimeStats(self, features, progress, field):
220+
count = len(features)
221+
total = 100.0 / float(count)
222+
stat = QgsDateTimeStatisticalSummary()
223+
for current, ft in enumerate(features):
224+
stat.addValue(ft[field.name()])
225+
progress.setPercentage(int(current * total))
226+
stat.finalize()
227+
228+
self.setOutputValue(self.COUNT, stat.count())
229+
self.setOutputValue(self.UNIQUE, stat.countDistinct())
230+
self.setOutputValue(self.EMPTY, stat.countMissing())
231+
self.setOutputValue(self.FILLED, stat.count() - stat.countMissing())
232+
self.setOutputValue(self.MIN, stat.statistic(QgsDateTimeStatisticalSummary.Min))
233+
self.setOutputValue(self.MAX, stat.statistic(QgsDateTimeStatisticalSummary.Max))
234+
235+
data = []
236+
data.append(self.tr('Count: {}').format(count))
237+
data.append(self.tr('Unique values: {}').format(stat.countDistinct()))
238+
data.append(self.tr('NULL (missing) values: {}').format(stat.countMissing()))
239+
data.append(self.tr('Minimum value: {}').format(field.displayString(stat.statistic(QgsDateTimeStatisticalSummary.Min))))
240+
data.append(self.tr('Maximum value: {}').format(field.displayString(stat.statistic(QgsDateTimeStatisticalSummary.Max))))
241+
242+
return data
243+
244+
def createHTML(self, outputFile, algData):
245+
with codecs.open(outputFile, 'w', encoding='utf-8') as f:
246+
f.write('<html><head>\n')
247+
f.write('<meta http-equiv="Content-Type" content="text/html; \
248+
charset=utf-8" /></head><body>\n')
249+
for s in algData:
250+
f.write('<p>' + str(s) + '</p>\n')
251+
f.write('</body></html>\n')

‎python/plugins/processing/algs/qgis/BasicStatisticsNumbers.py

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@@ -68,12 +68,18 @@ class BasicStatisticsNumbers(GeoAlgorithm):
6868
NULLVALUES = 'NULLVALUES'
6969
IQR = 'IQR'
7070

71+
def __init__(self):
72+
GeoAlgorithm.__init__(self)
73+
# this algorithm is deprecated - use BasicStatistics instead
74+
self.showInToolbox = False
75+
7176
def getIcon(self):
7277
return QIcon(os.path.join(pluginPath, 'images', 'ftools', 'basic_statistics.png'))
7378

7479
def defineCharacteristics(self):
7580
self.name, self.i18n_name = self.trAlgorithm('Basic statistics for numeric fields')
7681
self.group, self.i18n_group = self.trAlgorithm('Vector table tools')
82+
self.tags = self.tr('stats,statistics,number,table,layer')
7783

7884
self.addParameter(ParameterTable(self.INPUT_LAYER,
7985
self.tr('Input vector layer')))

‎python/plugins/processing/algs/qgis/BasicStatisticsStrings.py

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@@ -60,12 +60,18 @@ class BasicStatisticsStrings(GeoAlgorithm):
6060
MIN_VALUE = 'MIN_VALUE'
6161
MAX_VALUE = 'MAX_VALUE'
6262

63+
def __init__(self):
64+
GeoAlgorithm.__init__(self)
65+
# this algorithm is deprecated - use BasicStatistics instead
66+
self.showInToolbox = False
67+
6368
def getIcon(self):
6469
return QIcon(os.path.join(pluginPath, 'images', 'ftools', 'basic_statistics.png'))
6570

6671
def defineCharacteristics(self):
6772
self.name, self.i18n_name = self.trAlgorithm('Basic statistics for text fields')
6873
self.group, self.i18n_group = self.trAlgorithm('Vector table tools')
74+
self.tags = self.tr('stats,statistics,string,table,layer')
6975

7076
self.addParameter(ParameterTable(self.INPUT_LAYER,
7177
self.tr('Input vector layer')))

‎python/plugins/processing/algs/qgis/QGISAlgorithmProvider.py

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@@ -180,6 +180,7 @@
180180
from .PoleOfInaccessibility import PoleOfInaccessibility
181181
from .CreateAttributeIndex import CreateAttributeIndex
182182
from .DropGeometry import DropGeometry
183+
from .BasicStatistics import BasicStatisticsForField
183184

184185
pluginPath = os.path.normpath(os.path.join(
185186
os.path.split(os.path.dirname(__file__))[0], os.pardir))
@@ -243,7 +244,8 @@ def __init__(self):
243244
TinInterpolationZValue(), TinInterpolationAttribute(),
244245
RemoveNullGeometry(), ExtractByExpression(), ExtendLines(),
245246
ExtractSpecificNodes(), GeometryByExpression(), SnapGeometriesToLayer(),
246-
PoleOfInaccessibility(), CreateAttributeIndex(), DropGeometry()
247+
PoleOfInaccessibility(), CreateAttributeIndex(), DropGeometry(),
248+
BasicStatisticsForField()
247249
]
248250

249251
if hasMatplotlib:

‎python/plugins/processing/tests/testdata/custom/datetimes.dat

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‎python/plugins/processing/tests/testdata/custom/datetimes.id

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‎python/plugins/processing/tests/testdata/custom/datetimes.map

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‎python/plugins/processing/tests/testdata/custom/datetimes.tab

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!table
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!version 900
3+
!charset Neutral
4+
5+
Definition Table
6+
Type NATIVE Charset "Neutral"
7+
Fields 3
8+
date Date ;
9+
time Time ;
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date_time DateTime ;

‎python/plugins/processing/tests/testdata/expected/basic_statistics_date.html

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1+
<html><head>
2+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /></head><body>
3+
<p>Analyzed layer: custom/datetimes.tab</p>
4+
<p>Analyzed field: date</p>
5+
<p>Count: 4</p>
6+
<p>Unique values: 3</p>
7+
<p>NULL (missing) values: 1</p>
8+
<p>Minimum value: 2014-11-30T00:00:00</p>
9+
<p>Maximum value: 2016-11-30T00:00:00</p>
10+
</body></html>

‎python/plugins/processing/tests/testdata/expected/basic_statistics_datetime.html

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1+
<html><head>
2+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /></head><body>
3+
<p>Analyzed layer: custom/datetimes.tab</p>
4+
<p>Analyzed field: date_time</p>
5+
<p>Count: 4</p>
6+
<p>Unique values: 3</p>
7+
<p>NULL (missing) values: 1</p>
8+
<p>Minimum value: 2014-11-30T14:30:02</p>
9+
<p>Maximum value: 2016-11-30T14:29:22</p>
10+
</body></html>

‎python/plugins/processing/tests/testdata/expected/basic_statistics_time.html

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<html><head>
2+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /></head><body>
3+
<p>Analyzed layer: custom/datetimes.tab</p>
4+
<p>Analyzed field: time</p>
5+
<p>Count: 4</p>
6+
<p>Unique values: 3</p>
7+
<p>NULL (missing) values: 1</p>
8+
<p>Minimum value: 03:29:40</p>
9+
<p>Maximum value: 15:29:22</p>
10+
</body></html>

‎python/plugins/processing/tests/testdata/qgis_algorithm_tests.yaml

Lines changed: 74 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -152,7 +152,7 @@ tests:
152152
fields:
153153
fid: skip
154154

155-
- algorithm: qgis:basicstatisticsfornumericfields
155+
- algorithm: qgis:basicstatisticsforfields
156156
name: Basic statistics for numeric fields
157157
params:
158158
- name: multipolys.gml
@@ -182,7 +182,7 @@ tests:
182182
- 'NULL \(missing\) values: 1'
183183
- 'Interquartile Range \(IQR\): 0.123'
184184

185-
- algorithm: qgis:basicstatisticsfortextfields
185+
- algorithm: qgis:basicstatisticsforfields
186186
name: Basic statistics for text fields
187187
params:
188188
- name: multipolys.gml
@@ -191,7 +191,18 @@ tests:
191191
results:
192192
OUTPUT_HTML_FILE:
193193
name: expected/basic_statistics_string.html
194-
type: file
194+
type: regex
195+
rules:
196+
- 'Analyzed layer: multipolys.gml'
197+
- 'Analyzed field: Bname'
198+
- 'Count: 4'
199+
- 'Unique values: 2'
200+
- 'Minimum value: Test'
201+
- 'Maximum value: Test'
202+
- 'Minimum length: 0'
203+
- 'Maximum length: 4'
204+
- 'Mean length: 3.0'
205+
- 'NULL \(missing\) values: 1'
195206

196207
# Split lines with lines considers two cases
197208
# case 1: two different layers
@@ -1753,3 +1764,63 @@ tests:
17531764
OUTPUT:
17541765
name: expected/removed_holes_min_area.gml
17551766
type: vector
1767+
1768+
- algorithm: qgis:basicstatisticsforfields
1769+
name: Basic stats datetime
1770+
params:
1771+
FIELD_NAME: date_time
1772+
INPUT_LAYER:
1773+
name: custom/datetimes.tab
1774+
type: table
1775+
results:
1776+
OUTPUT_HTML_FILE:
1777+
name: expected/basic_statistics_datetime.html
1778+
type: regex
1779+
rules:
1780+
- 'Analyzed layer: custom/datetimes.tab'
1781+
- 'Analyzed field: date_time'
1782+
- 'Count: 4'
1783+
- 'Unique values: 3'
1784+
- 'Minimum value: 2014-11-30T14:30:02'
1785+
- 'Maximum value: 2016-11-30T14:29:22'
1786+
- 'NULL \(missing\) values: 1'
1787+
1788+
- algorithm: qgis:basicstatisticsforfields
1789+
name: Basic stats date
1790+
params:
1791+
FIELD_NAME: date
1792+
INPUT_LAYER:
1793+
name: custom/datetimes.tab
1794+
type: table
1795+
results:
1796+
OUTPUT_HTML_FILE:
1797+
name: expected/basic_statistics_date.html
1798+
type: regex
1799+
rules:
1800+
- 'Analyzed layer: custom/datetimes.tab'
1801+
- 'Analyzed field: date'
1802+
- 'Count: 4'
1803+
- 'Unique values: 3'
1804+
- 'Minimum value: 2014-11-30T00:00:00'
1805+
- 'Maximum value: 2016-11-30T00:00:00'
1806+
- 'NULL \(missing\) values: 1'
1807+
1808+
- algorithm: qgis:basicstatisticsforfields
1809+
name: Basic stats time
1810+
params:
1811+
FIELD_NAME: time
1812+
INPUT_LAYER:
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name: custom/datetimes.tab
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type: table
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results:
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OUTPUT_HTML_FILE:
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name: expected/basic_statistics_time.html
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type: regex
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rules:
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- 'Analyzed layer: custom/datetimes.tab'
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- 'Analyzed field: time'
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- 'Count: 4'
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- 'Unique values: 3'
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- 'Minimum value: 03:29:40'
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- 'Maximum value: 15:29:22'
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- 'NULL \(missing\) values: 1'

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