How to use getrowcount method in pyatom
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Matrix.py
Source:Matrix.py 
1# Matrix.py2# This class represents matrix.3#from __future__ import division4from DataType import DataType5from Number import Number6import Vector7# Somehow this avoids import problems.8from types import IntType, FloatType, ListType9from mit.cadlab.dome3.objectmodel.dataobject import DomeMatrixData10from mit.cadlab.dome3.objectmodel.dataobject import DomeVectorData1112#Known Bugs::13#Odd rounding occurs if the value type is Integer/int and14#operations involve a Real/float151617from math import fabs, sqrt1819class Matrix(DataType, DomeMatrixData):20 # Object Creation and Representation Methods21 def __init__(self,value0=0, value1=1):22 self.dataType = "Matrix"23 # Input is a DomeMatrixData24 if isinstance(value0, DomeMatrixData):25 DomeMatrixData.__init__(self, value0)26 elif (type(value0)==IntType and type(value1)==IntType):27 # row and column size specified28 DomeMatrixData.__init__(self, value0, value1)2930 #def __del__(self):3132 def __repr__(self):33 return str(self.getData())3435 def __str__(self):36 return str(self.getData())3738 def __cmp__(self,other):39 raise TypeError(str(self)+' cmp '+str(other))4041 #def __hash__(self):4243 def __nonzero__(self):44 # Return 0 if all elements are 045 for i in range(self.getRowCount()):46 for j in range(self.getColumnCount()):47 if self[i][j] != 0:48 return 149 return 05051 # Methods for Attribute Access52 #def __getattr__(self, name):53 #def __setattr__(self, name, value):54 #def __delattr__(self, name):5556 # Methods for Sequence and Mapping57 #def __len__(self):5859 def __getitem__(self, key):60 #print ' key: ' + str(key)61 if key < self.getRowCount():62 #return self.getRow(key)63 #return Vector.Vector(v[key])64 #return self.getData()[key]65 # KJT: changed return type from that above to that below66 return self.getData()[key]67 else:68 raise IndexError('Index '+str(key)+' out of range')6970 #def __setitem__(self, key, value):71 # print '...... setitem key: ' + str(key)72 # if key < self.getRowCount():73 # print '.... 2! setitem key: ' + str(key)74 # self.setItem(key, value)75 #else:76 # raise IndexError('Index '+str(key)+' out of range')7778 #def __delitem__(self, key):79 #def __getslice__(self,i,j,s):80 #def __setslice__(self,i,j,s):81 #def __delslice__(self,i,j):82 #def __contains__(self,obj):83848586 # Mathematical Operations methods87 def __add__(self,other):88 try:89 return self._add(other)90 except TypeError, e:91 try:92 return other.__radd__(self)93 except:94 raise e9596 def __sub__(self,other):97 try:98 return self._sub(other)99 except TypeError, e:100 try:101 return other.__rsub__(self)102 except:103 raise e104105 def __mul__(self,other):106 try:107 return self._mul(other)108 except TypeError, e:109 try:110 return other.__rmul__(self)111 except:112 raise e113114 def __div__(self,other):115 try:116 return self._div(other)117 except TypeError, e:118 try:119 return other.__rdiv__(self)120 except:121 raise e122123 #def __mod__(self,other):124 #def __divmod__(self,other):125 #def __pow__(self,other):126 #def __lshift__(self,other):127 #def __rshift__(self,other):128 #def __and__(self,other):129 #def __or__(self,other):130 #def __xor__(self,other):131 #def __radd__(self,other):132 #def __rsub__(self,other):133134 def __radd__(self,other):135 try:136 return self._add(other)137 except TypeError, e:138 try:139 return other.__radd__(self)140 except:141 raise e142143 def __rsub__(self,other):144 try:145 return self._sub(other)146 except TypeError, e:147 try:148 return other.__rsub__(self)149 except:150 raise e151152 def __rmul__(self,other):153 # case of scalar multiplication154 try:155 return self._mul(other)156 except TypeError, e:157 try:158 # is this a loop?159 return other.__rmul__(self)160 except:161 raise e162163164 def __rdiv__(self,other):165 raise TypeError("Cannot divide by a matrix.")166167 #def __rmod__(self,other):168 #def __rdivmod__(self,other):169 #def __rpow__(self,other):170 #def __rlshift__(self,other):171 #def __rrshift__(self,other):172 #def __rand__(self,other):173 #def __ror__(self,other):174 #def __rxor__(self,other):175 #def __iadd__(self,other):176 #def __isub__(self,other):177 #def __imul__(self,other):178 #def __idiv__(self,other):179 #def __imod__(self,other):180 #def __ipow__(self,other):181 #def __ilshift__(self,other):182 #def __irshift__(self,other):183 #def __iand__(self,other):184 #def __ior__(self,other):185 #def __ixor__(self,other):186187 def __neg__(self):188 return self*-1189190 #def __pos__(self):191 #def __abs__(self):192 #def __invert__(self):193 #def __int__(self):194 #def __long__(self):195 #def __float__(self):196 #def __complex__(self):197 #def __oct__(self):198 #def __hex__(self):199 #def __coerce__(self,other):200201202 # Comparison Operations203 #def __lt__(self,other):204 #def __le__(self,other):205 #def __gt__(self,other):206 #def __ge__(self,other):207208 def __eq__(self,other):209 #print '__eq__'210 if (isinstance(other,Matrix)) and (self.getRowCount()==other.getRowCount()) and (self.getColumnCount()==other.getColumnCount()):211 for i in range(self.getRowCount()):212 for j in range(self.getColumnCount()):213 if self[i][j] != other[i][j]:214 #print '... mismatch: ' + ' i=' + str(i) + ' j=' + str(j) + ' ' +str(self[i][j]) + ' ' + str(other[i][j])215 return 0216 return 1217 else:218 return 0219220 def __ne__(self,other):221 if (isinstance(other,Matrix)) and (self.getRowCount()==other.getRowCount()) and (self.getColumnCount()==other.getColumnCount()):222 for i in range(self.getRowCount()):223 for j in range(self.getColumnCount()):224 if self[i][j] != other[i][j]:225 return 1226 return 0227 else:228 return 1229230 # Overidding methods of DataType231 def _copyTo(self,other):232 # not implemented233 #if isinstance(other,Matrix):234 # other.value=self.value235 #else:236 DataType._copyTo(self,other)237238 # shallow copy239 def _copyFrom(self,other):240 if isinstance(other,Matrix):241 # check the size of other matrix if it's important.242 if self.isFixedSize() and ((self.getRowCount()!= other.getRowCount()) or (self.getColumnCount() != other.getColumnCount())):243 raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')244 else:245 self.setValueType(other.getValueType())246 # setData updates the units, initialValue, isFixedSize,247 self.setData(other)248 elif isinstance(other, Vector.Vector):249 if self.isFixedSize() and (self.getRowCount()!=other.getSize()) or (self.getColumnCount()!=1):250 raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')251 elif self.isFixedSize() and (self.getColumnCount()!=other.getSize()) or (self.getRowCount()!=1):252 raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')253 elif (self.isFixedSize() and self.getColumnCount()==1):254 self.setValueType(other.getValueType())255 self.setUnit(other.getUnit())256 self.setInitialValue(other.getInitialValue())257 self.setFixedSize(other.getFixedSize())258 for i in range(other.getSize()):259 self[i][0] = other[i]260 elif (self.isFixedSize() and self.getRowCount()==1):261 self.setValueType(other.getValueType())262 self.setUnit(other.getUnit())263 self.setInitialValue(other.getInitialValue())264 self.setFixedSize(other.getFixedSize())265 for i in range(other.getSize()):266 self[0][i] = other[i]267 else:268 self.setValueType(other.getValueType())269 self.setRowCount(1);270 self.setColumnCount(other.getSize());271 self.setUnit(other.getUnit())272 self.setInitialValue(other.getInitialValue())273 self.setFixedSize(other.getFixedSize())274 for i in range(other.getSize()):275 self[0][i] = other[i]276 elif isinstance(other, ListType):277 if self.isFixedSize() and (self.getRowCount()!=len(other)) or (self.getColumnCount()!=1):278 raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')279 elif self.isFixedSize() and (self.getColumnCount()!=len(other)) or (self.getRowCount()!=1):280 raise ValueError(str(self)+' copyFrom '+str(other)+': mis-matched sizes')281 elif (self.isFixedSize() and self.getColumnCount()==1):282 self.setValueType(other.getValueType())283 self.setUnit(other.getUnit())284 self.setInitialValue(other.getInitialValue())285 self.setFixedSize(other.getFixedSize())286 for i in range(len(other)):287 self[i][0] = other[i]288 elif (self.isFixedSize() and self.getRowCount()==1):289 self.setValueType(other.getValueType())290 self.setUnit(other.getUnit())291 self.setInitialValue(other.getInitialValue())292 self.setFixedSize(other.getFixedSize())293 for i in range(len(other)):294 self[0][i] = other[i]295 else:296 self.setValueType(other.getValueType())297 self.setRowCount(1);298 self.setColumnCount(len(other));299 self.setUnit(other.getUnit())300 self.setInitialValue(other.getInitialValue())301 self.setFixedSize(other.getFixedSize())302 for i in range(len(other)):303 self[0][i] = other[i]304 else:305 # raises TypeError306 DataType._copyFrom(self,other)307308309 def dup(self):310 # return a copy of one self311 #return Matrix(self.duplicate())312 # !!!!!!!! deep copy in Java is broken !!!!!!313 returnMatrix=Matrix(self.getRowCount(),self.getColumnCount())314 for i in range(self.getRowCount()):315 for j in range(self.getColumnCount()):316 if isNumberType(self[i][j]):317 returnMatrix[i][j]=self[i][j]318 else:319 returnMatrix[i][j]=self[i][j].dup()320 returnMatrix.setUnit(self.getUnit())321 returnMatrix.setInitialValue(self.getInitialValue())322 returnMatrix.setFixedSize(self.isFixedSize())323 returnMatrix.setValueType(self.getValueType())324 return returnMatrix325326327 # Matrix specific functions, probably will move to DMath.py328 def inverse(self):329 # eee... implement Gauss-Jordan elimination?330 # first matrix must be square331 if (not self.isSquare()):332 raise ValueError(str(self)+' must be sqaure to have an inverse.')333 elif (self.det()==0):334 raise ValueError(str(self)+' is not invertible, determinant == 0.')335 else:336 dim = self.getRowCount();337 augMatrix = self.catH(self.IdentityMatrix(dim,338 dim))339340 gauss = augMatrix.gaussianElimination()341 #print '.....Finished gaussian Elimination(): ' + str(gauss)342 # divide through by pivots343 #print '..... size of gauss, rows:' + str(gauss.getRowCount()) + ' cols:' + str(gauss.getColumnCount())344 for i in range(dim):345 pivot = gauss[i][i]346 #print '....pivot=' + str(pivot) + ' i=' + str(i)347 for j in range(2*dim):348 #print '.... j=' + str(j)349 #print '.......' + str(gauss[i][j])350 gauss[i][j]=gauss[i][j]/pivot351 if gauss[i][j] == 0:352 gauss[i][j] = 0353 return gauss.subMatrix(0, dim, dim-1, 2*dim-1)354355 def gaussianElimination(self):356 returnMatrix = self.dup()357 if (returnMatrix.getValueType()=='Integer'):358 returnMatrix.setValueType('real')359 diagonal = self.getColumnCount()360 if (self.getRowCount()<self.getColumnCount()):361 diagonal = self.getRowCount()362 for j in range(diagonal):363 rowIndex = returnMatrix._rowMax(j)364 returnMatrix._rowSwap(j, rowIndex)365 if (returnMatrix[j][j]==0.0):366 return Matrix(0,0)367 for k in range(self.getRowCount()):368 if (k!=j):369 returnMatrix._rowZero(j,j,k)370 return returnMatrix371372373 def catH(self, other):374 # return matrix of [self, other]375 # make sure the number of rows are equal376 ### MAYBE should use the java super's appendHorizontally()377 if not(isinstance(other, Matrix)):378 raise TypeError(str(other)+' is not a Matrix and cannnot be used in catH.')379 elif (self.getRowCount() != other.getRowCount()):380 raise ValueError(str(self)+' catH '+str(other)+' row number not the same.')381 else:382 tRow = self.getRowCount()383 tCol = self.getColumnCount() + other.getColumnCount()384 returnMatrix = Matrix(tRow, tCol)385 for i in range(tRow):386 for j in range(tCol):387 if j < self.getColumnCount():388 returnMatrix[i][j] = self[i][j]389 else:390 returnMatrix[i][j]=other[i][j-self.getColumnCount()]391 return returnMatrix392393 def catV(self, other):394 # return matrix of [self; other]395 # make sure the number of rows are equal396 ### MAYBE should use the java super's appendVertically()397 if not(isinstance(other, Matrix)):398 raise TypeError(str(other)+' is not a Matrix and cannnot be used in catV.')399 elif (self.getColumnCount() != other.getColumnCount()):400 raise ValueError(str(self)+' catV '+str(other)+' column number not the same.')401 else:402 tRow = self.getRowCount() + other.getRowCount()403 tCol = self.getColumnCount()404 returnMatrix = Matrix(tRow, tCol)405 for i in range(tRow):406 for j in range(tCol):407 if i < self.getRowCount():408 returnMatrix[i][j] = self[i][j]409 else:410 returnMatrix[i][j]=other[i-self.getRowCount()][j]411 return returnMatrix412413414415 def IdentityMatrix(self, rowCount, colCount):416 # errr, as close as it can get if it's not nxn.417 if (not(type(rowCount)==IntType) or not(type(colCount)==IntType)):418 raise TypeError(str(rowCount)+' or '+str(colCount)+' are not integer types')419 returnMatrix = Matrix(rowCount, colCount)420 cC=0421 for rC in range(rowCount):422 returnMatrix[rC][cC]=1423 cC=cC+1424 if cC >= colCount:425 return returnMatrix426 return returnMatrix427428 def transpose(self):429 # rows vs. columns.430 returnMatrix = Matrix(self.getColumnCount(), self.getRowCount())431 for i in range(self.getRowCount()):432 for j in range(self.getColumnCount()):433 returnMatrix[j][i] = self[i][j]434 return returnMatrix435436 def rowEchelon(self):437 numSwaps = 0438 return self._fwdElimination(numSwaps)[0]439440441442 def subMatrix(self, r1, c1, r2, c2):443 if r2 < r1:444 rHold = r2445 r2 = r1446 r1 = rHold447 if c2 < c1:448 cHold = c2449 c2 = c1450 c1 = cHold451 subRow = r2-r1+1452 subCol = c2-c1+1453 if (r2 < self.getRowCount()) and (c2 < self.getColumnCount()) and r1>=0 and r2 >=0:454 returnMatrix = Matrix(subRow, subCol)455 i2 = 0456 for i in range(r1,r2+1):457 j2 = 0458 for j in range(c1,c2+1):459 returnMatrix[i2][j2] = self[i][j]460 j2 = j2+1461 i2 = i2+1462 return returnMatrix463 else:464 raise IndexError('Indices not in range.')465466 def det(self):467 changedType = 0;468 if (self.isEmpty() or (not self.isSquare())):469 #print ' self is empty or not square'470 return 0.0471 if (self.getRowCount()==1):472 #print ' row count == 1'473 return self[0][0]474 if (self.getRowCount()==2):475 #print ' row count == 2'476 return ((self[0][0]*self[1][1])-(self[1][0]*self[0][1]))477 # matrix is not Empty, is Square, rows>2, use fwdElimination478 numSwaps = 0479 mtmp = self._fwdElimination(numSwaps)480 m = mtmp[0]481 numSwaps = mtmp[1]482 #print 'numSwaps: ' + str(numSwaps)483 if (m.isEmpty()):484 #print 'm is empty'485 return 0.0486 result = 1.0487 for i in range(self.getColumnCount()):488 result *= m[i][i]489 factor = -1490 if (numSwaps%2)==0:491 1492 result *= factor493 #print ' result: ' + str(result)494 return result495496497 def trace(self):498 result = 0.0499 diagonal = self.getColumnCount()500 if (self.getRowCount()<self.getColumnCount()):501 diagonal = self.getRowCount()502 for i in range(diagonal):503 result += self[i][i]504 return result505506507 def euclidNorm(self):508 return sqrt(self.sumOfSquares())509510511 def sumOfSquares(self):512 result = 0.0513 rows = self.getRowCount()514 cols = self.getColumnCount()515 value = 0.0516 for i in range(rows):517 for j in range(cols):518 value = self[i][j]519 result += value*value520 return result521522523 def absSum(self):524 result = 0.0525 for i in range(self.getRowCount()):526 for j in range(self.getColumnCount()):527 result += abs(self[i][j])528 return result529530531 def fill(self, value):532 # integer, real, float, int533 rows = self.getRowCount()534 cols = self.getColumnCount()535 if (isinstance(value, Number)):536 value = value.getValue()537 try:538 #print '...fill value: ' + str(value)539 for i in range(rows):540 for j in range(cols):541 #self.setItem(i,j,value)542 self[i][j] = value543 except TypeError, e:544 raise e545546 def getRow(self, index):547 # KJT, replaced following with line below: returnRow = self[index].dup()548 returnRow = DomeMatrixData.getRow(self, index)549 returnRow.setUnit(self.getUnit())550 return returnRow551552 def getCol(self, index):553 returnCol = DomeMatrixData.getCol(self, index)554 returnCol.setUnit(self.getUnit())555 return returnCol556 #KJT: changed implementation from that below to that above557 #returnVector = Vector.Vector()558 #returnVector.setSize(self.getRowCount())559 #returnVector.setValueType(self.getValueType())560 #returnVector.setInitialValue(self.getInitialValue())561 #returnVector.setUnit(self.getUnit())562 # assuming this is a column vector563 #for i in range(self.getRowCount()):564 # returnVector[i] = self[i][index]565 #return returnVector566567568 def numRows(self):569 return self.getRowCount()570571 def numCols(self):572 return self.getRowCount()573574 def size(self):575 return [self.getRowCount(), self.getColumnCount()]576 #KJT return self.getRowCount() * self.getColumnCount()577578 #def setSize(self, rows, cols):579 # self.setRowCount(rows)580 # self.setColumnCount(cols)581582 def setSize(self, rows, cols, value=0):583 oldRow = self.getRowCount()584 oldCol = self.getColumnCount()585 self.setRowCount(rows)586 self.setColumnCount(cols)587 if rows > oldRow:588 #print '...... set value of extra row'589 for i in range(oldRow, rows):590 for j in range(cols):591 #print 'i='+str(i)+' j='+str(j)+' val='+str(value)592 self[i][j] = value593 if cols > oldCol:594 #print '.... set value of extra col'595 for j in range(oldCol, cols):596 for i in range(rows):597 #print 'i='+str(i)+ ' j=' + str(j) + ' val=' + str(value)598 self[i][j] = value599600601 def setNumRows(self, rows, value=0):602 oldRow = self.getRowCount()603 self.setRowCount(rows)604 if rows > oldRow:605 for i in range(oldRow, rows):606 for j in range(self.getColumnCount()):607 self[i][j] = value608 #print 'i='+str(i)+' j='+ str(j)+' val='+str(value)609610611 def setNumCols(self, cols, value=0):612 oldCol = self.getColumnCount()613 self.setColumnCount(cols)614 if cols > oldCol:615 for j in range(oldCol, cols):616 for i in range(self.getRowCount()):617 self[i][j] = value618 #print 'i='+str(i)+' j='+str(j)+' val='+str(value)619620621 def setRow(self, index, value):622 if (not (isinstance(value, Vector.Vector))):623 raise TypeError('setRow(), ' +str(value)+': is not a Vector')624 if (value.getSize() != self.getColumnCount()) :625 raise ValueError('setRow(), '+str(value)+': mis-matched sizes')626 if (index >= self.getRowCount()):627 raise ValueError('setRow(), '+str(index)+': index out of range')628 else:629 for j in range(self.getColumnCount()):630 self[index][j] = value[j]631632633 def setCol(self, index, value):634 if (not (isinstance(value, Vector.Vector))):635 raise TypeError('setCol(), ' +str(value)+': is not a Vector')636 if (value.getSize() != self.getRowCount()) :637 raise ValueError('setCol(), '+str(value)+': mis-matched sizes')638 if (index >= self.getColumnCount()):639 raise ValueError('setCol(), '+str(index)+': index out of range')640 else:641 for i in range(self.getRowCount()):642 self[i][index] = value[i]643644 # Undefined645 def euclideanNorm():646 return sqrt(self.sumOfSquares())647648649650 # Actually implementation of mathematical operators651 def _add(self,other):652 if (isinstance(other, Number)):653 # scalar add654 returnMatrix = self.dup()655 if (isinstance(other, Real)):656 # automatically change return matrix type to real657 returnMatrix.setValueType("real")658 for i in range(returnMatrix.getRowCount()):659 for j in range(returnMatrix.getColumnCount()):660 returnMatrix[i][j] = returnMatrix[i][j]+other.value661 elif isNumberType(other):662 #scalar add663 returnMatrix = self.dup()664 if (type(other)==FloatType):665 # automatically change return matrix type to real666 returnMatrix.setValueType("real")667 for i in range(returnMatrix.getRowCount()):668 for j in range(returnMatrix.getColumnCount()):669 returnMatrix[i][j] = returnMatrix[i][j]+other670 return returnMatrix671 elif isinstance(other, Matrix):672 # check the size of other matrix673 if (self.getRowCount()== other.getRowCount()) and (self.getColumnCount() == other.getColumnCount()):674 returnMatrix = self.dup()675 for i in range(returnMatrix.getRowCount()):676 for j in range(returnMatrix.getColumnCount()):677 returnMatrix[i][j] = returnMatrix[i][j]+other[i][j]678 if (other.getValueType()=='real'):679 returnMatrix.setValueType('real')680 return returnMatrix681 else:682 raise ValueError(str(self)+' + '+str(other)+': mis-matched sizes')683 elif isinstance(other, Vector.Vector):684 if (self.getRowCount()==other.getSize()) and (self.getColumnCount()==1):685 returnMatrix = self.dup()686 for i in range(other.getSize()):687 returnMatrix[i][0] = returnMatrix[i][0] + other[i]688 return returnMatrix689 elif (self.getColumnCount()==other.getSize()) and (self.getRowCount()==1):690 returnMatrix = self.dup()691 for i in range(other.getSize()):692 returnMatrix[0][i] = returnMatrix[0][i] + other[i]693 return returnMatrix694 else:695 raise ValueError(str(self)+' + '+str(other)+': mis-matched sizes')696 elif isinstance(other, ListType):697 if ((self.getRowCount()==len(other)) and (self.getColumnCount()==1)):698 returnMatrix = self.dup()699 for i in range(len(other)):700 returnMatrix[i][0] = returnMatrix[i][0]+other[i]701 return returnMatrix702 elif (self.getColumnCount()==len(other)) and (self.getRowCount()==1):703 returnMatrix = self.dup()704 for i in range(len(other)):705 returnMatrix[0][i] = returnMatrix[0][i]+other[i]706 return returnMatrix707 else:708 raise ValueError(str(self)+' + '+str(other)+': mis-matched sizes')709710 else:711 raise TypeError('Matrix cannot be added to with '+712 other.getClass().getName())713714 def _sub(self,other):715 if isinstance(other, Number):716 #scalar sub717 returnMatrix = self.dup()718 for i in range(returnMatrix.getRowCount()):719 for j in range(returnMatrix.getColumnCount()):720 returnMatrix[i][j] = returnMatrix[i][j]-other.value721 elif isNumberType(other):722 #scalar sub723 returnMatrix = self.dup()724 for i in range(returnMatrix.getRowCount()):725 for j in range(returnMatrix.getColumnCount()):726 returnMatrix[i][j] = returnMatrix[i][j]-other727 return returnMatrix728 elif isinstance(other, Matrix):729 # check the size of other matrix730 if (self.getRowCount()== other.getRowCount()) and (self.getColumnCount() == other.getColumnCount()):731 returnMatrix = self.dup()732 for i in range(returnMatrix.getRowCount()):733 for j in range(returnMatrix.getColumnCount()):734 returnMatrix[i][j] = returnMatrix[i][j]-other[i][j]735 return returnMatrix736 else:737 raise ValueError(str(self)+' - '+str(other)+': mis-matched sizes')738 elif isinstance(other, Vector.Vector):739 if (self.getRowCount()==other.getSize()) and (self.getColumnCount()==1):740 returnMatrix = self.dup()741 for i in range(other.getSize()):742 returnMatrix[i][0] = returnMatrix[i][0] - other[i]743 return returnMatrix744 elif (self.getColumnCount()==other.getSize()) and (self.getRowCount()==1):745 returnMatrix = self.dup()746 for i in range(other.getSize()):747 returnMatrix[0][i] = returnMatrix[0][i] - other[i]748 return returnMatrix749 else:750 raise ValueError(str(self)+' - '+str(other)+': mis-matched sizes')751 elif isinstance(other, ListType):752 if ((self.getRowCount()==len(other)) and (self.getColumnCount()==1)):753 returnMatrix = self.dup()754 for i in range(len(other)):755 returnMatrix[i][0] = returnMatrix[i][0]-other[i]756 return returnMatrix757 elif (self.getColumnCount()==len(other)) and (self.getRowCount()==1):758 returnMatrix = self.dup()759 for i in range(len(other)):760 returnMatrix[0][i] = returnMatrix[0][i]-other[i]761 return returnMatrix762 else:763 raise ValueError(str(self)+' - '+str(other)+': mis-matched sizes')764 else:765 raise TypeError('Matrix cannot be subtracted to with a '+766 other.getClass().getName())767768 def _mul(self,other):769 if isinstance(other, Number):770 #scalar multiplication771 returnMatrix = self.dup()772 for i in range(returnMatrix.getRowCount()):773 for j in range(returnMatrix.getColumnCount()):774 returnMatrix[i][j] = returnMatrix[i][j]*other.value775 elif isNumberType(other):776 #scalar multiplication777 returnMatrix = self.dup()778779 for i in range(returnMatrix.getRowCount()):780 for j in range(returnMatrix.getColumnCount()):781 returnMatrix[i][j] = returnMatrix[i][j]*other782 return returnMatrix783 elif isinstance(other, Matrix):784 # check the size of other matrix, size of rows == size of columns785 # or number of columns == # of rows786 if (self.getColumnCount()== other.getRowCount()):787 # return has self # rows and other # columns788 returnMatrix = Matrix(self.getRowCount(),789 other.getColumnCount())790 for i in range(returnMatrix.getRowCount()):791 for j in range(returnMatrix.getColumnCount()):792 entry = 0793 for sC in range(selfMatrix.getColumnCount()):794 for oR in range(selfMatrix.getRowCount()):795 entry = self[i][sC]*other[oR][j]+entry796 returnMatrix[i][j] = entry797 return returnMatrix798 else:799 raise ValueError(str(self)+' * '+str(other)+': mis-matched sizes')800 elif isinstance(other, Vector.Vector):801 # !!!! Need to worry about reverse, Vector * Matrix802 if (self.getColumnCount()==other.getSize()):803 returnMatrix = Matrix(self.getRowCount(),804 1)805806 for i in range(returnMatrix.getRowCount()):807 entry = 0808 for sC in range(returnMatrix.getColumnCount()):809 entry = self[0][sC]*other[sC] + entry810 returnMatrix[i][0] = entry811 return returnMatrix812 else:813 raise ValueError(str(self)+' * '+str(other)+': mis-matched sizes')814 elif isinstance(other, ListType):815 if (self.getColumnCount()==len(other)):816 returnMatrix = Matrix(self.getRowCount(),817 1)818 for i in range(returnMatrix.getRowCount()):819 entry = 0820 for sC in range(returnMatrix.getColumnCount):821 entry = self[0][sC]*other[sC] + entry822 returnMatrix[i][0] = entry823 return returnMatrix824 else:825 raise ValueError(str(self)+' * '+str(other)+': mis-matched sizes')826 else:827 raise TypeError('Matrix cannot be multiplied by a '+828 other.getClass().getName())829830831 def _div(self,other):832 if isinstance(other, Number):833 #scalar multiplication834 returnMatrix = self.dup()835 for i in range(returnMatrix.getRowCount()):836 for j in range(returnMatrix.getColumnCount()):837 returnMatrix[i][j] = returnMatrix[i][j]/other.value838 elif isNumberType(other):839 #like scalar multiplication840 returnMatrix = self.dup()841842 for i in range(returnMatrix.getRowCount()):843 for j in range(returnMatrix.getColumnCount()):844 returnMatrix[i][j] = returnMatrix[i][j]/other845 return returnMatrix846 else:847 raise TypeError('Matrix cannot be divided by a '+848 other.getClass().getName())849850851 # Need to change852 #def _pow(self,other):853 #def __radd__(self,other):854 #def __rsub__(self,other):855 #def __rmul__(self,other):856 #def __rdiv__(self,other):857 #def __rmod__(self,other):858 #def __rpow__(self,other):859 #def __neg__(self):860 #def __pos__(self):861 #def __abs__(self):862 #def __int__(self):863 #def __float__(self):864 #def __long__(self):865 #def __complex__(self):866867868 # Undocumented helper functions869 def isEmpty(self):870 return (self.getRowCount()==0) or (self.getColumnCount()==0)871872 def isSquare(self):873 return self.getRowCount()==self.getColumnCount()874875 def isUpperTriangular(self):876 if (self.isEmpty()):877 return false878 rows = self.getRowCount()879 cols = self.getColumnCount()880 for i in range(1,rows):881 #if ((i<cols)&&((self[i][i]==0)) return false882 j = 0883 while (j<i) and (j<cols):884 if (self[i][j]!=0):885 return false886 j=j+1887 return true888889 def isNonSingular(self):890 if (self.isEmpty()):891 return false892 if (self.isUpperTriangular()):893 diagonal = self.getColumnCount()894 if (self.getRowCount()<self.getColumnCount()):895 diagonal = self.getRowCount()896 index = 0897 while (index<diagonal):898 if (self[index][index]==0):899 return false900 index=index+1901 return true902 rowEchelonForm = self.rowEchelon()903 rowEchelonForm.isNonSingular()904905906907908 # private helper functions doing row manipulations909910 def _fwdElimination(self, numSwaps):911 # numSwaps should be an int912 returnMatrix = self.dup()913 if (returnMatrix.getValueType() == 'Integer'):914 returnMatrix.setValueType('real')915 rows = self.getRowCount()916 cols = self.getColumnCount()917 diagonal = cols918 if (rows<cols):919 diagonal = rows920 numSwaps=0921 for j in range(diagonal):922 numSwaps += returnMatrix._rowSwap(j, returnMatrix._rowMax(j))923 if (returnMatrix[j][j]==0):924 #print 'found a 0 on the diagonal'925 # Not certain if this is what we really want to return...926 return [Matrix(0,0), numSwaps]927 for k in range(j+1, rows):928 #print '.... returnMatrix after rowSwap:' + str(returnMatrix)929 returnMatrix._rowZero(j,j,k)930 #print 'k=' + str(k) + ' matrix:' + str(returnMatrix)931 #print '???? ' + str(returnMatrix)932 return [returnMatrix, numSwaps]933934 def _rowSwap(self, r1, r2):935 # r1, r2 are int936 # assert r1 and r2 are valid937 if (r1==r2):938 return 0939 numCols = self.getColumnCount()940 tmp = 0.0941 for j in range(numCols):942 tmp = self[r1][j]943 self[r1][j]=self[r2][j]944 self[r2][j]=tmp945 return 1946947 def _rowScale(self, rIndex, factor):948 # rIndex is int, factor is real949 numCols = self.getColumnCount()950 for j in range(numCols):951 self[rIndex][j]*=factor952953 def _rowZero(self, col, r1, r2):954 # assert col, r1 and r2 are valid955 # adding a multiple of r1 to r2, r1 is left unchanged956 #print ' numerator: ' + str(self[r2][col])957 #print ' denominator ' + str(self[r1][col])958 numerator = float(self[r2][col])959 denominator = float(self[r1][col])960 factor = -1.0*(numerator/denominator)961 #print '_rowZero factor=' + str(factor) +' col=' + str(col) + ' r1='+ str(r1) + ' r2=' + str(r2)962 numCols = self.getColumnCount()963 for j in range(numCols):964 self[r2][j] += self[r1][j]*factor965 #print ' after rowZero: ' + str(self)966967968 def _rowMax(self, c):969 # returns number of row with highest absolute value in specified970 # column971 # starts searching at r=c972 # assert c is valid973 # c is an int974 r = c975 result = r976 #print '_rowMax c = ' + str(c)977 maxValue = fabs(self[result][c])978 #print '.... init maxValue ' + str(maxValue) + ' init result ' + str(result)979 for i in range(r, self.getRowCount()):980 #while r<self.getRowCount():981 currentValue = fabs(self[i][c])982 #print '...... currentValue at ' + str(i) + ' is:' + str(currentValue)983 if (currentValue > maxValue):984 result = i985 maxValue = currentValue986 #print '_rowMax result=' + str(result)987 return result988989990991 # Conversion functions992993 def array(self):994 returnList = []995 for i in range(self.getRowCount()):996 returnList.append(self[i].array())997 return returnList9989991000100110021003#Helper functions1004def isNumberType(x):1005 return type(x)==IntType or type(x)==FloatType100610071008
...
test_session.py
Source:test_session.py
1# Copyright (C) 2018-2021 CS GROUP - France. All Rights Reserved.2#3# This file is part of the Prewikka program.4#5# SPDX-License-Identifier: BSD-2-Clause6#7# Redistribution and use in source and binary forms, with or without8# modification, are permitted provided that the following conditions are met:9#10# 1. Redistributions of source code must retain the above copyright notice, this11# list of conditions and the following disclaimer.12#13# 2. Redistributions in binary form must reproduce the above copyright notice,14# this list of conditions and the following disclaimer in the documentation15# and/or other materials provided with the distribution.16#17# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND18# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIEDi19# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE20# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR21# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES22# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;23# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND24# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT25# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS26# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.27"""28Tests for `prewikka.session.session`.29"""30from copy import deepcopy31import datetime32import time33from http import cookies34import pytest35from prewikka.config import ConfigSection36from prewikka.session.session import SessionInvalid, SessionExpired, SessionDatabase, Session37from prewikka.usergroup import User38from tests.fixtures import TEST_SESSION_ID39from tests.tests_session.utils import FakeAuthBackend, create_session, clean_sessions40def test_session_invalid():41 """42 Test `prewikka.session.session.SessionInvalid` error.43 """44 session_invalid = SessionInvalid()45 with pytest.raises(SessionInvalid):46 raise session_invalid47 session_invalid = SessionInvalid(login='test')48 with pytest.raises(SessionInvalid):49 raise session_invalid50def test_session_expired():51 """52 Test `prewikka.session.session.SessionExpired` error.53 """54 session_expired = SessionExpired()55 with pytest.raises(SessionExpired):56 raise session_expired57 session_expired = SessionExpired(login='test')58 with pytest.raises(SessionExpired):59 raise session_expired60def test_session_db_create_():61 """62 Test `prewikka.session.session.SessionDatabase.create_session` method.63 """64 user = User('anonymous')65 session_id = create_session(user)66 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)67 assert query.getRowCount() == 168 assert session_id in query.toString()69 assert user.name in query.toString()70 clean_sessions()71def test_session_db_update():72 """73 Test `prewikka.session.session.SessionDatabase.update_session` method.74 """75 session_database = SessionDatabase()76 user = User('anonymous')77 session_id = create_session(user)78 old_query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)79 time_ = time.time() + 3600 # add 3600s80 session_database.update_session(session_id, time_)81 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)82 assert old_query.toString() != query.toString()83 assert query.getRowCount() == 184 assert session_id in query.toString()85 assert user.name in query.toString()86 assert datetime.datetime.utcfromtimestamp(time_).strftime('%Y-%m-%d %H:%M:%S')in query.toString()87 # wrong session_id: nothing happening88 fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'89 session_database.update_session(fake_session_id, time_)90 clean_sessions()91def test_session_db_get():92 """93 Test `prewikka.session.session.SessionDatabase.get_session` method.94 """95 session_database = SessionDatabase()96 user = User('anonymous')97 session_id = create_session(user)98 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)99 assert query.getRowCount() == 1100 username, time_ = session_database.get_session(session_id)101 assert username == user.name102 assert datetime.datetime.utcfromtimestamp(time_).strftime('%Y-%m-%d %H:%M:%S')in query.toString()103 # wrong session_id: fail104 with pytest.raises(Exception):105 fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'106 session_database.get_session(fake_session_id)107 clean_sessions()108def test_session_db_delete():109 """110 Test `prewikka.session.session.SessionDatabase.delete_session` method.111 """112 session_database = SessionDatabase()113 user = User('anonymous')114 # delete 1 session based on sessionid115 session_id = create_session(user)116 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)117 assert query.getRowCount() == 1118 session_database.delete_session(sessionid=session_id)119 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)120 assert query.getRowCount() == 0121 # delete 1 session based on userid122 session_id = create_session(user)123 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)124 assert session_id in query.toString()125 assert query.getRowCount() == 1126 session_database.delete_session(user=user)127 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)128 assert query.getRowCount() == 0129 # delete multiple sessions based on userid130 session_id_1 = create_session(user)131 session_id_2 = create_session(user)132 session_id_3 = create_session(user)133 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)134 assert session_id_1 in query.toString()135 assert session_id_2 in query.toString()136 assert session_id_3 in query.toString()137 assert query.getRowCount() == 3138 session_database.delete_session(user=user)139 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)140 assert query.getRowCount() == 0141 clean_sessions()142 # delete session based on invalid sessionid: nothing happening143 create_session(user)144 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)145 assert query.getRowCount() == 1146 fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'147 session_database.delete_session(sessionid=fake_session_id)148 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)149 assert query.getRowCount() == 1150 # delete session based on invalid userid: nothing happening151 fake_user = User('fake')152 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', fake_user.id)153 assert query.getRowCount() == 0154 session_database.delete_session(user=fake_user)155 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)156 assert query.getRowCount() == 1157 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', fake_user.id)158 assert query.getRowCount() == 0159 # delete session with both userid and sessionid: fail160 with pytest.raises(Exception):161 fake_session_id = 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'162 fake_user_id = 'bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb'163 session_database.delete_session(sessionid=fake_session_id, user=fake_user_id)164 # delete session without userid and sessionid: nothing165 session_database.delete_session(sessionid=None, user=None)166 clean_sessions()167def test_session_db_delete_expired_():168 """169 Test `prewikka.session.session.SessionDatabase.delete_expired_sessions` method.170 """171 session_database = SessionDatabase()172 user = User('anonymous')173 t_now = time.time()174 t_before = t_now - 3600175 t_after = t_now + 3600176 # without sessions in database177 session_database.delete_expired_sessions(t_now)178 # with 1 session expired in database179 session_id = create_session(user, t_before)180 session_database.delete_expired_sessions(t_now)181 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)182 assert query.getRowCount() == 0183 # with 1 session NOT expired in database184 session_id = create_session(user, t_after)185 session_database.delete_expired_sessions(t_now)186 query = env.db.query('SELECT * from Prewikka_Session WHERE sessionid=%s', session_id)187 assert query.getRowCount() == 1188 clean_sessions()189 # with 2 sessions expired and 1 not expired190 session_id_1 = create_session(user, t_before)191 session_id_2 = create_session(user, t_before)192 session_id_3 = create_session(user, t_after)193 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)194 assert query.getRowCount() == 3195 session_database.delete_expired_sessions(t_now)196 query = env.db.query('SELECT * from Prewikka_Session WHERE userid=%s', user.id)197 assert query.getRowCount() == 1198 assert session_id_1 not in query.toString()199 assert session_id_2 not in query.toString()200 assert session_id_3 in query.toString()201 clean_sessions()202def test_session():203 """204 Test `prewikka.session.session.Session` class.205 """206 session_config = ConfigSection("")207 session_config.expiration = 60 # 1 hour208 create_session(env.request.user, session_id=TEST_SESSION_ID)209 req = deepcopy(env.request.web)210 # __init__()211 session = Session(session_config)212 # get_user()213 user_from_session = session.get_user(req)214 assert env.request.user == user_from_session215 # get_user() with old (but valid) cookie216 clean_sessions()217 create_session(env.request.user, time_=time.time()-3600, session_id=TEST_SESSION_ID)218 user_from_session = session.get_user(req)219 assert env.request.user == user_from_session220 # get_user() with invalid session (empty cookie)221 with pytest.raises(SessionInvalid):222 req = deepcopy(env.request.web)223 req.input_cookie = {}224 session.get_user(req)225 # get_user() with expired session (AJAX request)226 with pytest.raises(SessionExpired):227 req = deepcopy(env.request.web)228 req.input_cookie = {}229 req.is_xhr = True230 session.get_user(req)231 # get_user() with invalid session (bad session_id)232 with pytest.raises(SessionInvalid):233 req = deepcopy(env.request.web)234 req.input_cookie['sessionid'] = cookies.Morsel()235 req.input_cookie['sessionid'].value = 'invalid'236 session.get_user(req)237 # get_user() with expired session (cookie expired)238 with pytest.raises(SessionExpired):239 clean_sessions()240 req = deepcopy(env.request.web)241 create_session(env.request.user, time_=time.time()-3600*24, session_id=TEST_SESSION_ID)242 session = Session(session_config)243 session.get_user(req)244 # get_user() with invalid user245 backup_user = env.request.user246 with pytest.raises(SessionInvalid):247 req = deepcopy(env.request.web)248 env.request.user = User('test')249 session.get_user(req)250 env.request.user = backup_user251 # get_user() with changed backend252 backup_auth = env.auth253 with pytest.raises(SessionInvalid):254 req = deepcopy(env.request.web)255 clean_sessions()256 create_session(env.request.user, session_id=TEST_SESSION_ID)257 env.auth = FakeAuthBackend(ConfigSection(""))258 session.get_user(req)259 env.auth = backup_auth260 # logout()261 with pytest.raises(SessionInvalid):262 clean_sessions()263 create_session(env.request.user, session_id=TEST_SESSION_ID)264 session = Session(session_config)265 req = deepcopy(env.request.web)266 session.logout(req)267 # can_logout()268 assert session.can_logout()...
ParseBED.py
Source:ParseBED.py
1from __future__ import print_function2# This file is part of DQXServer - (C) Copyright 2014, Paul Vauterin, Ben Jeffery, Alistair Miles <info@cggh.org>3# This program is free software licensed under the GNU Affero General Public License.4# You can find a copy of this license in LICENSE in the top directory of the source code or at <http://opensource.org/licenses/AGPL-3.0>5from builtins import str6from DQXTableUtils import VTTable7import sys8basepath = '.'9#============= FAKE STUFF FOR DEBUGGING; REMOVE FOR PRODUCTION ==============10if True:11 basepath = '/Users/pvaut/Documents/Genome/SnpCrossData3'12 sys.argv = ['', 'genomeregions.bed']13#============= END OF FAKE STUFF ============================================14if len(sys.argv)<2:15 print('Usage: COMMAND BEDFileName')16 sys.exit()17sourcefile = sys.argv[1]18tb = VTTable.VTTable()19tb.AddColumn(VTTable.VTColumn('chromid', 'Text'))20tb.AddColumn(VTTable.VTColumn('fstart', 'Value'))21tb.AddColumn(VTTable.VTColumn('fend', 'Value'))22tb.AddColumn(VTTable.VTColumn('fname', 'Text'))23tb.AddColumn(VTTable.VTColumn('fid', 'Text'))24tb.AddColumn(VTTable.VTColumn('ftype', 'Text'))25tb.AddColumn(VTTable.VTColumn('fparentid', 'Text'))26tb.AddColumn(VTTable.VTColumn('fnames', 'Text'))27tb.AddColumn(VTTable.VTColumn('descr', 'Text'))28nr = 029with open(basepath + '/' + sourcefile, 'r') as fp:30 for line in fp:31 tokens = line.rstrip('\r\n').split('\t')32 print(str(tokens))33 tb.AddRowEmpty()34 tb.SetValue(tb.GetRowCount()-1, 0, tokens[0])35 tb.SetValue(tb.GetRowCount()-1, 1, int(tokens[1]))36 tb.SetValue(tb.GetRowCount()-1, 2, int(tokens[2]))37 tb.SetValue(tb.GetRowCount()-1, 3, tokens[3])38 tb.SetValue(tb.GetRowCount()-1, 4, str(nr))39 tb.SetValue(tb.GetRowCount()-1, 5, 'region')40 tb.SetValue(tb.GetRowCount()-1, 6, '')41 tb.SetValue(tb.GetRowCount()-1, 7, '')42 tb.SetValue(tb.GetRowCount()-1, 8, '')43 nr += 144tb.PrintRows(0, 9)45tb.SaveSQLCreation(basepath + '/' + sourcefile +'.create.sql', 'regions')...
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