Annotation of /trunk/gadget/stray.cc

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1 :	agomez	1	#include "stray.h"
2 :			#include "errorhandler.h"
3 :			#include "keeper.h"
4 :			#include "areatime.h"
5 :			#include "mathfunc.h"
6 :			#include "readfunc.h"
7 :			#include "readword.h"
8 :			#include "readaggregation.h"
9 :			#include "gadget.h"
10 :			#include "global.h"
11 :
12 :			StrayData::StrayData(CommentStream& infile, const LengthGroupDivision* const lgrpdiv,
13 :			const IntVector& areas, const AreaClass* const Area, const char* givenname,
14 :			const TimeClass* const TimeInfo, Keeper* const keeper) : HasName(givenname), LivesOnAreas(areas) {
15 :
16 :			keeper->addString("stray");
17 :			int i, tmpint = 0;
18 :			istagged = 0;
19 :			ratioscale = 1.0; //JMB used to scale the ratios to ensure that they sum to 1
20 :
21 :			char text[MaxStrLength];
22 :			strncpy(text, "", MaxStrLength);
23 :			ifstream datafile;
24 :			CommentStream subdata(datafile);
25 :
26 :			LgrpDiv = new LengthGroupDivision(*lgrpdiv);
27 :			if (LgrpDiv->Error())
28 :			handle.logMessage(LOGFAIL, "Error in straying data - failed to create length group");
29 :			strayProportion.resize(LgrpDiv->numLengthGroups(), 0.0);
30 :
31 :			infile >> text >> ws;
32 :			if ((strcasecmp(text, "straystep") != 0) && (strcasecmp(text, "straysteps") != 0))
33 :			handle.logFileUnexpected(LOGFAIL, "straysteps", text);
34 :
35 :			while (isdigit(infile.peek()) && !infile.eof()) {
36 :			infile >> tmpint >> ws;
37 :			strayStep.resize(1, tmpint);
38 :			}
39 :
40 :			for (i = 0; i < strayStep.Size(); i++)
41 :			if (strayStep[i] < 1 || strayStep[i] > TimeInfo->numSteps())
42 :			handle.logFileMessage(LOGFAIL, "invalid straying step", strayStep[i]);
43 :
44 :			infile >> text >> ws;
45 :			if ((strcasecmp(text, "strayarea") != 0) && (strcasecmp(text, "strayareas") != 0))
46 :			handle.logFileUnexpected(LOGFAIL, "strayareas", text);
47 :
48 :			while (isdigit(infile.peek()) && !infile.eof()) {
49 :			infile >> tmpint >> ws;
50 :			strayArea.resize(1, tmpint);
51 :			}
52 :
53 :			for (i = 0; i < strayArea.Size(); i++)
54 :			strayArea[i] = Area->getInnerArea(strayArea[i]);
55 :
56 :			infile >> text >> ws;
57 :			if (strcasecmp(text, "straystocksandratios") != 0)
58 :			handle.logFileUnexpected(LOGFAIL, "straystocksandratios", text);
59 :
60 :			i = 0;
61 :			infile >> text >> ws;
62 :			while (strcasecmp(text, "proportionfunction") != 0 && !infile.eof()) {
63 :			strayStockNames.resize(new char[strlen(text) + 1]);
64 :			strcpy(strayStockNames[i], text);
65 :			strayRatio.resize(1, keeper);
66 :			if (!(infile >> strayRatio[i]))
67 :			handle.logFileMessage(LOGFAIL, "invalid format for stray ratio");
68 :			strayRatio[i].Inform(keeper);
69 :
70 :			infile >> text >> ws;
71 :			i++;
72 :			}
73 :
74 :			if (infile.eof())
75 :			handle.logFileEOFMessage(LOGFAIL);
76 :			if (strcasecmp(text, "proportionfunction") != 0)
77 :			handle.logFileUnexpected(LOGFAIL, "proportionfunction", text);
78 :
79 :			infile >> text >> ws;
80 :			if (strcasecmp(text, "constant") == 0)
81 :			fnProportion = new ConstSelectFunc();
82 :			else if (strcasecmp(text, "straightline") == 0)
83 :			fnProportion = new StraightSelectFunc();
84 :			else if (strcasecmp(text, "exponential") == 0)
85 :			fnProportion = new ExpSelectFunc();
86 :			else
87 :			handle.logFileMessage(LOGFAIL, "unrecognised proportion function", text);
88 :
89 :			fnProportion->readConstants(infile, TimeInfo, keeper);
90 :
91 :			infile >> ws;
92 :			if (!infile.eof()) {
93 :			infile >> text >> ws;
94 :			handle.logFileUnexpected(LOGFAIL, "<end of file>", text);
95 :			}
96 :			handle.logMessage(LOGMESSAGE, "Read straying data file");
97 :			keeper->clearLast();
98 :			}
99 :
100 :			StrayData::~StrayData() {
101 :			int i;
102 :			for (i = 0; i < strayStockNames.Size(); i++)
103 :			delete[] strayStockNames[i];
104 :			for (i = 0; i < CI.Size(); i++)
105 :			delete CI[i];
106 :			delete LgrpDiv;
107 :			delete fnProportion;
108 :			}
109 :
110 :			void StrayData::setStock(StockPtrVector& stockvec) {
111 :			int i, j, index;
112 :
113 :			for (i = 0; i < strayStockNames.Size(); i++)
114 :			for (j = 0; j < strayStockNames.Size(); j++)
115 :			if ((strcasecmp(strayStockNames[i], strayStockNames[j]) == 0) && (i != j))
116 :			handle.logMessage(LOGFAIL, "Error in straying data - repeated stock", strayStockNames[i]);
117 :
118 :			for (i = 0; i < stockvec.Size(); i++)
119 :			for (j = 0; j < strayStockNames.Size(); j++)
120 :			if (strcasecmp(stockvec[i]->getName(), strayStockNames[j]) == 0)
121 :			strayStocks.resize(stockvec[i]);
122 :
123 :			if (strayStocks.Size() != strayStockNames.Size()) {
124 :			handle.logMessage(LOGWARN, "Error in straying data - failed to match straying stocks");
125 :			for (i = 0; i < stockvec.Size(); i++)
126 :			handle.logMessage(LOGWARN, "Error in straying data - found stock", stockvec[i]->getName());
127 :			for (i = 0; i < strayStockNames.Size(); i++)
128 :			handle.logMessage(LOGWARN, "Error in straying data - looking for stock", strayStockNames[i]);
129 :			handle.logMessage(LOGFAIL, ""); //JMB this will exit gadget
130 :			}
131 :
132 :			//JMB ensure that the ratio vector is indexed in the right order
133 :			ratioindex.resize(strayStocks.Size(), 0);
134 :			for (i = 0; i < strayStocks.Size(); i++)
135 :			for (j = 0; j < strayStockNames.Size(); j++)
136 :			if (strcasecmp(strayStocks[i]->getName(), strayStockNames[j]) == 0)
137 :			ratioindex[i] = j;
138 :
139 :			//JMB check that the straying stocks are defined on all the areas
140 :			int minStrayAge = 9999;
141 :			int maxStrayAge = 0;
142 :			double minlength = 9999.0;
143 :			for (i = 0; i < strayStocks.Size(); i++) {
144 :			CI.resize(new ConversionIndex(LgrpDiv, strayStocks[i]->getLengthGroupDiv()));
145 :			if (CI[i]->Error())
146 :			handle.logMessage(LOGFAIL, "Error in straying data - error when checking length structure");
147 :			index = 0;
148 :			for (j = 0; j < strayArea.Size(); j++)
149 :			if (!strayStocks[i]->isInArea(strayArea[j]))
150 :			index++;
151 :
152 :			if (index != 0)
153 :			handle.logMessage(LOGWARN, "Warning in straying data - straying stock isnt defined on all areas");
154 :
155 :			minStrayAge = min(strayStocks[i]->minAge(), minStrayAge);
156 :			maxStrayAge = max(strayStocks[i]->maxAge(), maxStrayAge);
157 :			minlength = min(strayStocks[i]->getLengthGroupDiv()->minLength(), minlength);
158 :			}
159 :
160 :			minStrayLength = LgrpDiv->numLengthGroup(minlength);
161 :			IntVector minlv(maxStrayAge - minStrayAge + 1, 0);
162 :			IntVector sizev(maxStrayAge - minStrayAge + 1, LgrpDiv->numLengthGroups());
163 :			Storage.resize(areas.Size(), minStrayAge, minlv, sizev);
164 :			for (i = 0; i < Storage.Size(); i++)
165 :			Storage[i].setToZero();
166 :			}
167 :
168 :			void StrayData::storeStrayingStock(int area, AgeBandMatrix& Alkeys, const TimeClass* const TimeInfo) {
169 :
170 :			int age, len;
171 :			int inarea = this->areaNum(area);
172 :			double straynumber;
173 :
174 :			for (age = Storage[inarea].minAge(); age < Storage[inarea].maxAge(); age++) {
175 :			for (len = Storage[inarea].minLength(age); len < Storage[inarea].maxLength(age); len++) {
176 :			straynumber = Alkeys[age][len].N * strayProportion[len];
177 :			Storage[inarea][age][len].N = straynumber;
178 :			Storage[inarea][age][len].W = Alkeys[age][len].W;
179 :
180 :			if (len >= minStrayLength)
181 :			Alkeys[age][len].N -= straynumber;
182 :			}
183 :			}
184 :			}
185 :
186 :			void StrayData::storeStrayingStock(int area, AgeBandMatrix& Alkeys,
187 :			AgeBandMatrixRatio& TagAlkeys, const TimeClass* const TimeInfo) {
188 :
189 :			if (!istagged)
190 :			handle.logMessage(LOGFAIL, "Error in stray - invalid tagging experiment");
191 :
192 :			int age, len, tag;
193 :			int inarea = this->areaNum(area);
194 :			double straynumber;
195 :
196 :			for (age = Storage[inarea].minAge(); age < Storage[inarea].maxAge(); age++) {
197 :			for (len = Storage[inarea].minLength(age); len < Storage[inarea].maxLength(age); len++) {
198 :			straynumber = Alkeys[age][len].N * strayProportion[len];
199 :			Storage[inarea][age][len].N = straynumber;
200 :			Storage[inarea][age][len].W = Alkeys[age][len].W;
201 :
202 :			if (len >= minStrayLength)
203 :			Alkeys[age][len].N -= straynumber;
204 :
205 :			for (tag = 0; tag < TagAlkeys.numTagExperiments(); tag++) {
206 :			straynumber = *(TagAlkeys[age][len][tag].N) * strayProportion[len];
207 :			if (straynumber < verysmall)
208 :			*(tagStorage[inarea][age][len][tag].N) = 0.0;
209 :			else
210 :			*(tagStorage[inarea][age][len][tag].N) = straynumber;
211 :
212 :			if (len >= minStrayLength)
213 :			*(TagAlkeys[age][len][tag].N) -= straynumber;
214 :			}
215 :			}
216 :			}
217 :			}
218 :
219 :			void StrayData::addStrayStock(int area, const TimeClass* const TimeInfo) {
220 :
221 :			int i, inarea = this->areaNum(area);
222 :			double ratio;
223 :			for (i = 0; i < strayStocks.Size(); i++) {
224 :			if (!strayStocks[i]->isInArea(area))
225 :			handle.logMessage(LOGFAIL, "Error in straying - stray stock doesnt live on area", area);
226 :
227 :			if (strayStocks[i]->isBirthday(TimeInfo)) {
228 :			Storage[inarea].IncrementAge();
229 :			if (istagged && tagStorage.numTagExperiments() > 0)
230 :			tagStorage[inarea].IncrementAge(Storage[inarea]);
231 :			}
232 :
233 :			ratio = strayRatio[ratioindex[i]] * ratioscale;
234 :			strayStocks[i]->Add(Storage[inarea], CI[i], area, ratio);
235 :			if (istagged && tagStorage.numTagExperiments() > 0)
236 :			strayStocks[i]->Add(tagStorage, CI[i], area, ratio);
237 :			}
238 :			Storage[inarea].setToZero();
239 :			if (istagged && tagStorage.numTagExperiments() > 0)
240 :			tagStorage[inarea].setToZero();
241 :			}
242 :
243 :			int StrayData::isStrayStepArea(int area, const TimeClass* const TimeInfo) {
244 :			int i, j;
245 :
246 :			for (i = 0; i < strayStep.Size(); i++)
247 :			for (j = 0; j < strayArea.Size(); j++)
248 :			if ((strayStep[i] == TimeInfo->getStep()) && (strayArea[j] == area))
249 :			return 1;
250 :			return 0;
251 :			}
252 :
253 :			void StrayData::Reset(const TimeClass* const TimeInfo) {
254 :			int i;
255 :
256 :			//JMB check that the sum of the ratios is 1
257 :			if (TimeInfo->getTime() == 1) {
258 :			ratioscale = 0.0;
259 :			for (i = 0; i < strayRatio.Size(); i++ )
260 :			ratioscale += strayRatio[i];
261 :
262 :			if (isZero(ratioscale)) {
263 :			handle.logMessage(LOGWARN, "Warning in straying - specified ratios are zero");
264 :			ratioscale = 1.0;
265 :			} else if (isEqual(ratioscale, 1.0)) {
266 :			// do nothing
267 :			} else {
268 :			handle.logMessage(LOGWARN, "Warning in straying - scaling ratios using", ratioscale);
269 :			ratioscale = 1.0 / ratioscale;
270 :			}
271 :			}
272 :
273 :			fnProportion->updateConstants(TimeInfo);
274 :			if (fnProportion->didChange(TimeInfo)) {
275 :			for (i = 0; i < LgrpDiv->numLengthGroups(); i++) {
276 :			strayProportion[i] = fnProportion->calculate(LgrpDiv->meanLength(i));
277 :			if (strayProportion[i] < 0.0) {
278 :			handle.logMessage(LOGWARN, "Warning in straying - function outside bounds", strayProportion[i]);
279 :			strayProportion[i] = 0.0;
280 :			}
281 :			if (strayProportion[i] > 1.0) {
282 :			handle.logMessage(LOGWARN, "Warning in straying - function outside bounds", strayProportion[i]);
283 :			strayProportion[i] = 1.0;
284 :			}
285 :			}
286 :
287 :			if (handle.getLogLevel() >= LOGMESSAGE)
288 :			handle.logMessage(LOGMESSAGE, "Reset straying data for stock", this->getName());
289 :			}
290 :			}
291 :
292 :			void StrayData::Print(ofstream& outfile) const {
293 :			int i;
294 :			outfile << "\nStraying information\n\tNames of straying stocks:";
295 :			for (i = 0; i < strayStockNames.Size(); i++)
296 :			outfile << sep << strayStockNames[i];
297 :			outfile << "\n\tRatio moving into each stock:";
298 :			for (i = 0; i < strayRatio.Size(); i++)
299 :			outfile << sep << (strayRatio[ratioindex[i]] * ratioscale);
300 :			outfile << "\n\tStraying timesteps:";
301 :			for (i = 0; i < strayStep.Size(); i++)
302 :			outfile << sep << strayStep[i];
303 :			outfile << endl;
304 :			}
305 :
306 :			const StockPtrVector& StrayData::getStrayStocks() {
307 :			return strayStocks;
308 :			}
309 :
310 :			void StrayData::setTagged() {
311 :			istagged = 1;
312 :			//resize tagStorage to be the same size as Storage
313 :			int i, minage, maxage;
314 :			minage = Storage[0].minAge();
315 :			maxage = Storage[0].maxAge();
316 :			IntVector lower(maxage - minage + 1, 0);
317 :			IntVector size(maxage - minage + 1, LgrpDiv->numLengthGroups());
318 :			tagStorage.resize(areas.Size(), minage, lower, size);
319 :			for (i = 0; i < tagStorage.Size(); i++)
320 :			tagStorage[i].setToZero();
321 :			}
322 :
323 :			void StrayData::addStrayTag(const char* tagname) {
324 :			if (!istagged)
325 :			handle.logMessage(LOGFAIL, "Error in stray - invalid tagging experiment", tagname);
326 :			tagStorage.addTag(tagname);
327 :			}
328 :
329 :			void StrayData::deleteStrayTag(const char* tagname) {
330 :			if (!istagged)
331 :			handle.logMessage(LOGFAIL, "Error in stray - invalid tagging experiment", tagname);
332 :
333 :			int minage, maxage, age, len, a;
334 :			int id = tagStorage.getTagID(tagname);
335 :
336 :			if (id >= 0) {
337 :			minage = tagStorage[0].minAge();
338 :			maxage = tagStorage[0].maxAge();
339 :			//free memory allocated for tagging experiment
340 :			for (a = 0; a < tagStorage.Size(); a++) {
341 :			for (age = minage; age <= maxage; age++) {
342 :			for (len = tagStorage[a].minLength(age); len < tagStorage[a].maxLength(age); len++) {
343 :			delete[] (tagStorage[a][age][len][id].N);
344 :			(tagStorage[a][age][len][id].N) = NULL;
345 :			}
346 :			}
347 :			}
348 :			tagStorage.deleteTag(tagname);
349 :
350 :			} else
351 :			handle.logMessage(LOGWARN, "Warning in stray - failed to delete tagging experiment", tagname);
352 :			}

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