| @@ -1529,6 +1529,63 @@ |
| } |
| return leapYear; |
| } |
| + /** |
| + * Loops through and finds "m-day" consecutive values and takes the arithmetic average of them |
| + * @param flowData a string[][] containing: column1 = dates, column2 = flowValues |
| + * @param numDays an integer representing the number (m) of consecutive days to be desired for analysis |
| + * @returns an ArrayList containing an ArrayList of each set of "m-day" consecutive set of flows for analysis (min, max, average, etc) |
| + * @throws IOException |
| + */ |
| + public Object[] getMdayData(String[][] flowData, int numDays) throws IOException{ |
| + DoubleMath doubleMath = new DoubleMath(); |
| + |
| + //Loop through flow data and find "m"-day consecutive flows |
| + ArrayList<String> allDate = new ArrayList<String>(); |
| + ArrayList<Double> allData = new ArrayList<Double>(); |
| + try{ |
| + for(int i=0; i<flowData.length; i++){ |
| + ArrayList<String> mDayDate = new ArrayList<String>(); |
| + ArrayList<Double> mDayData = new ArrayList<Double>(); |
| + int ctr = i; |
| + for(int j=0; j<numDays; j++){ |
| + if(j==0){ |
| + //Keep the first day |
| + mDayDate.add(flowData[ctr][0]); |
| + mDayData.add(Double.parseDouble(flowData[ctr][1])); |
| + }else{ |
| + //Compare the current day to the previous day for consecutive-ness |
| + boolean checkNextDate = checkSubsequentDates(flowData[ctr-1][0], flowData[ctr][0]); |
| + if(checkNextDate){ |
| + mDayDate.add(flowData[ctr][0]); |
| + mDayData.add(Double.parseDouble(flowData[ctr][1])); |
| + }else{ |
| + //If not consecutive days, break out of the loop and move to the next date for flowData |
| + mDayDate.clear(); |
| + mDayData.clear(); |
| + i = ctr - 1;//Skip to newest date since there is a break in the consecutive day data |
| + break; |
| + } |
| + } |
| + ctr++; |
| + } |
| + if(mDayData.size() == numDays){ |
| + //Add this m-consecutive day set of data to the all data array list for statistics later |
| + String startDate = mDayDate.get(0); |
| + String endDate = mDayDate.get(numDays - 1); |
| + allDate.add(startDate + " to " + endDate); |
| + allData.add(doubleMath.meanArithmetic(mDayData)); |
| + } |
| + } |
| + }catch(ArrayIndexOutOfBoundsException e){ |
| + //If the consecutive day counter (ctr) goes beyond the length of data available, |
| + //stop the subroutine and return the existing results |
| + Object[] returnArray = {allDate, allData}; |
| + return returnArray; |
| + } |
| + |
| + Object[] returnArray = {allDate, allData}; |
| + return returnArray; |
| + } |
| // /** |
| // * Reduces all data to just that within the specified date range |
| // * @param allData all water quality data for the earlier provided date range and station ID (column1 = date, column2 = value) |
| @@ -187,8 +187,8 @@ |
| } |
| /** |
| * Calculates the arithmetic mean of the provided double[] array |
| - * @param data the double[] array of which the average is desired |
| - * @return the double value of the average of the data array |
| + * @param data the double[] array of which the arithmetic mean is desired |
| + * @return the double value of the arithmetic mean of the data array |
| */ |
| public double meanArithmetic(double[] data){ |
| //Calculates the average of a double array |
| @@ -203,8 +203,8 @@ |
| } |
| /** |
| * Calculates the arithmetic mean of the provided ArrayList<Double> |
| - * @param data the ArrayList<Double> of which the average is desired |
| - * @return the double value of the average of the data array |
| + * @param data the ArrayList<Double> of which the arithmetic mean is desired |
| + * @return the double value of the arithmetic mean of the data array |
| */ |
| public double meanArithmetic(ArrayList<Double> data){ |
| //Calculates the average of a double array |
| @@ -215,6 +215,32 @@ |
| return average; |
| } |
| /** |
| + * Calculates the harmonic mean of the provided double[] array, |
| + * only calculates for real positive values. |
| + * |
| + * Note that the final estimate of the harmonic mean is a weighted average |
| + * of the harmonic mean of the non-zero elements and zero. |
| + * @param data the double[] array of which the harmonic mean is desired |
| + * @return the double value of the harmonic mean of the data array |
| + */ |
| + public double meanHarmonic(double[] data){ |
| + //Calculate properties of harmonic mean |
| + double reciprocalSum = 0, nZeros = 0, nNonZeros = 0; |
| + for(int i=0; i<data.length; i++){ |
| + if(data[i] > 0){ |
| + reciprocalSum = reciprocalSum + (1/data[i]);//sum of reciprocals |
| + }else{ |
| + nZeros++; |
| + } |
| + nNonZeros++; |
| + } |
| + |
| + //Compute harmonic mean (with correction for the number of zero items in the array) |
| + double meanHarmonic = (nNonZeros - nZeros) / (reciprocalSum * ((nNonZeros - nZeros)/nNonZeros)); |
| + |
| + return meanHarmonic; |
| + } |
| + /** |
| * Finds the average of the Log10 of a double[] array |
| * @param data the double[] array that the average is desired for |
| * @return the double value of the average of the Log10 of the data array |
| @@ -74,7 +74,7 @@ |
| String period3End) throws IOException, ParseException{ |
| //Get today's date for output purposes |
| Date currentDate = new Date(); |
| - SimpleDateFormat desiredDateFormat = new SimpleDateFormat("yyyy-MM-dd"); |
| + SimpleDateFormat desiredDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm"); |
| String today = desiredDateFormat.format(currentDate); |
| stationName = stationName.replace(",", ""); |
| |
| @@ -253,8 +253,8 @@ |
| statsSummaryTable[165][0] = "December (Coefficient of Variation)"; |
| } |
| statsSummaryTable[statsSummaryTable.length - 4][0] = "Flow Statistics based on Indicators of Hydrologic Alteration from:"; |
| - statsSummaryTable[statsSummaryTable.length - 3][0] = "B.D. Richter; J.V. Baumgartner; J. Powell; D.P. Braun. 1996. 'A Method For Assessing Hydrologic Aleration Within Ecosystems.' Conservation Biology 10(4): 1163-1174.\t"; |
| - statsSummaryTable[statsSummaryTable.length - 2][0] = "B.D. Richter; J.V. Baumgartner; R. Wigington; D.P Braun. 1997. 'How Much Water Does A River Need?' Freshwater Biology. 37: 231-249.\t"; |
| + statsSummaryTable[statsSummaryTable.length - 3][0] = "B.D. Richter; J.V. Baumgartner; J. Powell; D.P. Braun. 1996. 'A Method For Assessing Hydrologic Aleration Within Ecosystems.' Conservation Biology 10(4): 1163-1174."; |
| + statsSummaryTable[statsSummaryTable.length - 2][0] = "B.D. Richter; J.V. Baumgartner; R. Wigington; D.P Braun. 1997. 'How Much Water Does A River Need?' Freshwater Biology. 37: 231-249."; |
| statsSummaryTable[statsSummaryTable.length - 1][0] = "B.D. Richter; J.V. Baumgartner; D.P. Braun; J. Powell. 1998. 'A Spatial Assessment Of Hydrologic Alteration Within A River Network.' Regul. Rivers: Res. Mgmt. 14: 329-340."; |
| |
| //Calculate all data statistics |
| @@ -446,17 +446,21 @@ |
| return returnArray; |
| } |
| /** |
| - * |
| - * @param statsSummaryTable |
| - * @param flowData |
| - * @param highPercentile |
| - * @param lowPercentile |
| - * @param m |
| - * @param dataHeader |
| - * @param showMonthlyTF |
| - * @param seasonBegin |
| - * @param seasonEnd |
| - * @return |
| + * calculates flow statistics for the provided flowData and appends the column |
| + * of results to the statsSummaryTable under the provided header |
| + * @param statsSummaryTable the summary table to add to |
| + * @param flowData the String[][] containing sorted data for the time series |
| + * (column 1 = dates (yyyy-mm-dd) column 2 = value |
| + * @param highPercentile the percentile value for defining a "high flow pulse" |
| + * typically greater than 75% = 0.75 |
| + * @param lowPercentile the percentile value for defining a "low flow pulse" |
| + * typically lower than 25% = 0.25 |
| + * @param m used to calculate an "m-day-average" minimum flow |
| + * @param dataHeader the text header for this column of result statistics in the statsSummaryTable (i.e. 'All Data' or '1998') |
| + * @param showMonthlyTF a flag to show monthly statistics (min/max/etc.) or not (which reduces the total output of the tool) |
| + * @param seasonBegin the month and date (MM-dd) of the start of a seasonal analysis to be averaged over the period of data |
| + * @param seasonEnd the month and date (MM-dd) of the end of a seasonal analysis to be averaged over the period of data |
| + * @return an Object[] containing the updated statsSummaryTable at returnObject[0] and the m-day-average minimum-flow at returnObject[1] |
| * @throws IOException |
| */ |
| private Object[] calculateFlowStatistics(String[][] statsSummaryTable, |
| @@ -596,7 +600,7 @@ |
| double centroid = centroidSum / sum; |
| |
| //Calculate 3-day statistics |
| - Object[] resultArray = getMdayData(flowData, 3); |
| + Object[] resultArray = doubleArray.getMdayData(flowData, 3); |
| ArrayList<String> average_3day_date = (ArrayList<String>) resultArray[0]; |
| ArrayList<Double> average_3day = (ArrayList<Double>) resultArray[1]; |
| double max_3day = doubleMath.max(average_3day); |
| @@ -605,7 +609,7 @@ |
| String min_3day_date = getDateOfValue(average_3day_date, average_3day, min_3day); |
| |
| //Calculate 7-day statistics |
| - resultArray = getMdayData(flowData, 7); |
| + resultArray = doubleArray.getMdayData(flowData, 7); |
| ArrayList<String> average_7day_date = (ArrayList<String>) resultArray[0]; |
| ArrayList<Double> average_7day = (ArrayList<Double>) resultArray[1]; |
| double max_7day = doubleMath.max(average_7day); |
| @@ -615,7 +619,7 @@ |
| String min_7day_date = getDateOfValue(average_7day_date, average_7day, min_7day); |
| |
| //Calculate 30-day statistics |
| - resultArray = getMdayData(flowData, 30); |
| + resultArray = doubleArray.getMdayData(flowData, 30); |
| ArrayList<String> average_30day_date = (ArrayList<String>) resultArray[0]; |
| ArrayList<Double> average_30day = (ArrayList<Double>) resultArray[1]; |
| double max_30day = doubleMath.max(average_30day); |
| @@ -624,7 +628,7 @@ |
| String min_30day_date = getDateOfValue(average_30day_date, average_30day, min_30day); |
| |
| //Calculate 90-day statistics |
| - resultArray = getMdayData(flowData, 90); |
| + resultArray = doubleArray.getMdayData(flowData, 90); |
| ArrayList<String> average_90day_date = (ArrayList<String>) resultArray[0]; |
| ArrayList<Double> average_90day = (ArrayList<Double>) resultArray[1]; |
| double max_90day = doubleMath.max(average_90day); |
| @@ -635,7 +639,7 @@ |
| //Calculate mQn (7Q10)Statistics |
| double min_Mday = 0; |
| if(m != 0){ |
| - resultArray = getMdayData(flowData, m); |
| + resultArray = doubleArray.getMdayData(flowData, m); |
| ArrayList<Double> average_Mday = (ArrayList<Double>) resultArray[1]; |
| min_Mday = doubleMath.min(average_Mday); |
| } |
| @@ -853,64 +857,6 @@ |
| return returnArray; |
| } |
| /** |
| - * Loops through and finds "m-day" consecutive values and takes the average of them |
| - * @param flowData a string[][] containing: column1 = dates, column2 = flowValues |
| - * @param numDays an integer representing the number (m) of consecutive days to be desired for analysis |
| - * @returns an ArrayList containing an ArrayList of each set of "m-day" consecutive set of flows for analysis (min, max, average, etc) |
| - * @throws IOException |
| - */ |
| - private Object[] getMdayData(String[][] flowData, int numDays) throws IOException{ |
| - DoubleMath doubleMath = new DoubleMath(); |
| - DoubleArray doubleArray = new DoubleArray(); |
| - |
| - //Loop through flow data and find "m"-day consecutive flows |
| - ArrayList<String> allDate = new ArrayList<String>(); |
| - ArrayList<Double> allData = new ArrayList<Double>(); |
| - try{ |
| - for(int i=0; i<flowData.length; i++){ |
| - ArrayList<String> mDayDate = new ArrayList<String>(); |
| - ArrayList<Double> mDayData = new ArrayList<Double>(); |
| - int ctr = i; |
| - for(int j=0; j<numDays; j++){ |
| - if(j==0){ |
| - //Keep the first day |
| - mDayDate.add(flowData[ctr][0]); |
| - mDayData.add(Double.parseDouble(flowData[ctr][1])); |
| - }else{ |
| - //Compare the current day to the previous day for consecutive-ness |
| - boolean checkNextDate = doubleArray.checkSubsequentDates(flowData[ctr-1][0], flowData[ctr][0]); |
| - if(checkNextDate){ |
| - mDayDate.add(flowData[ctr][0]); |
| - mDayData.add(Double.parseDouble(flowData[ctr][1])); |
| - }else{ |
| - //If not consecutive days, break out of the loop and move to the next date for flowData |
| - mDayDate.clear(); |
| - mDayData.clear(); |
| - i = ctr - 1;//Skip to newest date since there is a break in the consecutive day data |
| - break; |
| - } |
| - } |
| - ctr++; |
| - } |
| - if(mDayData.size() == numDays){ |
| - //Add this m-consecutive day set of data to the all data array list for statistics later |
| - String startDate = mDayDate.get(0); |
| - String endDate = mDayDate.get(numDays - 1); |
| - allDate.add(startDate + " to " + endDate); |
| - allData.add(doubleMath.meanArithmetic(mDayData)); |
| - } |
| - } |
| - }catch(ArrayIndexOutOfBoundsException e){ |
| - //If the consecutive day counter (ctr) goes beyond the length of data available, |
| - //stop the subroutine and return the existing results |
| - Object[] returnArray = {allDate, allData}; |
| - return returnArray; |
| - } |
| - |
| - Object[] returnArray = {allDate, allData}; |
| - return returnArray; |
| - } |
| - /** |
| * Loop through the provided data array and gets the corresponding index to 'value' and returns that index from the dates array |
| * @param dates a list of dates |
| * @param data a list of values corresponding to the dates in the above list |
| @@ -53,6 +53,7 @@ |
| String period3End = ""; |
| double highPercentile = 0.75; |
| double lowPercentile = 0.25; |
| + boolean showMonthlyStatsTF = false; |
| String mQnPeriod = "false";//"7Q10";// |
| String userData = "";//"Date\tFlow\n1999-04-29\t8.3\n1999-05-09\t60.2\n1999-05-29\t20.1$$Date\t00600\n1999-04-29\t8.3\n1999-05-09\t60.2\n1999-05-29\t20.1";//"Date\tFlow\n1999-04-29\t8.3\n1999-05-09\t60.2\n1999-05-29\t20.1";// |
| boolean mergeDatasets = false;//true;// |
| @@ -201,6 +202,9 @@ |
| public void setLowPercentile(double lowPercentile) { |
| this.lowPercentile = lowPercentile; |
| } |
| + public void setShowMonthlyStatsTF(boolean showMonthlyStatsTF) { |
| + this.showMonthlyStatsTF = showMonthlyStatsTF; |
| + } |
| public void setMQNperiod(String mQnPeriod) { |
| this.mQnPeriod = mQnPeriod; |
| } |
| @@ -292,7 +296,7 @@ |
| |
| //Calculate the flow stats file |
| FlowStatistics flowStats = new FlowStatistics(); |
| - Object[] returnValue = flowStats.calculateAllStatisticsSummaries(mainFolder, stationID, stationName, sortedData_combined, highPercentile, lowPercentile, m, n, true, |
| + Object[] returnValue = flowStats.calculateAllStatisticsSummaries(mainFolder, stationID, stationName, sortedData_combined, highPercentile, lowPercentile, m, n, showMonthlyStatsTF, |
| seasonBegin, seasonEnd, period1Begin, period1End, period2Begin, period2End, period3Begin, period3End); |
| double mQn = (Double) returnValue[0]; |
| String MQNmessage = (String) returnValue[1]; |
| @@ -677,7 +681,7 @@ |
| |
| //Calculate the flow stats file |
| FlowStatistics flowStats = new FlowStatistics(); |
| - Object[] returnValue = flowStats.calculateAllStatisticsSummaries(mainFolder, stationID, stationName, sortedData_combined, highPercentile, lowPercentile, m, n, true, |
| + Object[] returnValue = flowStats.calculateAllStatisticsSummaries(mainFolder, stationID, stationName, sortedData_combined, highPercentile, lowPercentile, m, n, showMonthlyStatsTF, |
| seasonBegin, seasonEnd, period1Begin, period1End, period2Begin, period2End, period3Begin, period3End); |
| double mQn = (Double) returnValue[0]; |
| String MQNmessage = (String) returnValue[1]; |
| @@ -69,6 +69,7 @@ |
| boolean medianTF = false; |
| double highPercentile = 0.75; |
| double lowPercentile = 0.25; |
| + boolean showMonthlyStatsTF = false; |
| String userData = "";//"Date\tFlow\n1999-04-29\t8.3\n1999-05-09\t60.2\n1999-05-29\t20.1";// |
| boolean mergeDatasets = false;//true;// |
| String mergeMethod = "user";//"public";//"max";//"average";//"min";// |
| @@ -413,6 +414,9 @@ |
| public void setLowPercentile(double lowPercentile) { |
| this.lowPercentile = lowPercentile; |
| } |
| + public void setShowMonthlyStatsTF(boolean showMonthlyStatsTF) { |
| + this.showMonthlyStatsTF = showMonthlyStatsTF; |
| + } |
| public void setUserData(String userData) { |
| this.userData = userData; |
| } |
| @@ -1828,7 +1832,7 @@ |
| FlowStatistics flowStats = new FlowStatistics(); |
| if(wqTest.equalsIgnoreCase("flow")){ |
| //Calculate Hydrologic Indicators of Alteration |
| - flowStats.calculateAllStatisticsSummaries(mainFolder, stationID, stationName, sortedData_combined, highPercentile, lowPercentile, 0, 0, true, |
| + flowStats.calculateAllStatisticsSummaries(mainFolder, stationID, stationName, sortedData_combined, highPercentile, lowPercentile, 0, 0, showMonthlyStatsTF, |
| seasonBegin, seasonEnd, period1Begin, period1End, period2Begin, period2End, period3Begin, period3End); |
| }else{ |
| //Report that there cannot be flow statistics for water quality data |