def __call__(self, **kwargs):
"""
Executes model
Args:
kwargs (dict, optional):
keyword arguments passed to pre(), control() and post()
silent (bool):
if True then suppress printing
Return:
(float):
residuum from range 0.0 .. 1.0 indicating error of task
or -1.0 if parallel and rank > 0
"""
# skip model execution if parallelized with MPI and rank > 0
if parallel.rank():
return -1.0
self.silent = kwargs.get('silent', self.silent)
self.prolog()
self.pre(**kwargs)
res = self.control(**kwargs)
self.post(**kwargs)
self.epilog()
return res
def write(self, *message):
"""
Sends output to console (if not in silent mode) and to log file of root
Wraps print() function considering indent of follower objects
Args:
message (list):
list of variable arguments to be written; if last argument is
'None', line wont be completed (no carriage return)
Note:
No seperator between print elements, comparable to print(x, sep='')
"""
silent = self.silent or parallel.rank()
lf = self._logFile
if lf is None:
lf = self.root()._logFile
if self._lineCompleted:
if not silent:
print(self.indent(), end='')
if lf:
print(self.indent(), end='', file=lf)
for x in message:
if x is not None:
if not silent:
print(str(x), end='', sep='')
if lf:
print(str(x), end='', sep='', file=lf)
if not message or message[-1] is not None:
if not silent:
print()
if lf:
print(file=lf)
self._lineCompleted = True
def auction(cost_dict, min_cost, max_cost, row_numbers, col_numbers):
"""Linear sum assignment procedure based on symetric auction algorithm.
Re-implementation of a FORTRAN code, taken from:
http://web.mit.edu/afs/athena.mit.edu/user/d/i/dimitrib/www/auction.txt
and as described in:
"Auction Algorithms for Network Flow Problems: A Tutorial Introduction"
Dimitri P. Bertsekas, Computational Optimization and Applications, Vol.
1, pp. 7-66, 1992.
and other papers by Dimitri P. Bertsekas, see:
http://www.mit.edu:8001//people/dimitrib/publ.html
Takes as input a cost dictionary, the minimum and maximum weights in this
dictionary, and two sorted lists with the row and column numbers.
"""
#################### START PARALLEL TEST CODE ###############################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = cost_dict.keys()
tmp_list.sort()
tmp_str = str(min_cost) + ' /' + str(max_cost)+', '+ str(row_numbers) + \
' / ' + str(col_numbers) + ':: '
for k in tmp_list:
tmp_list2 = cost_dict[k].items()
tmp_list2.sort()
tmp_str = tmp_str + ' ' + str(tmp_list2) + ' / '
f = open(
'lap-auction-' + str(parallel.rank()) + '-' + str(parallel.size()),
'a')
f.write(tmp_str + os.linesep)
f.close()
#################### END PARALLEL TEST CODE ###############################
i_large = 100000000 # A value larger than max_cost
auction_results = {} # Result dictionary with final record pair matches
num_rows = len(row_numbers)
num_cols = len(col_numbers)
if (num_rows != num_cols):
print 'error:Asymmetric problem given to symmetric "auction" algorithm'
raise Exception
# Set parameters for auction algorithm - - - - - - - - - - - - - - - - - - -
#
if (max_cost > int(i_large / (num_rows + 1))):
print 'error:Cost range too large to work with integer epsilon'
raise Exception
max_cost *= (num_rows + 1)
beg_eps = max_cost / 5 # Maybe smaller, can even be 1, but not smaller
end_eps = num_rows / 10 # Must be smaller than beg_eps, can be 1
if (end_eps < 1):
end_eps = 1
elif (end_eps > beg_eps):
end_eps = beg_eps
factor = 5 # Must be greater than 1
start_incr = beg_eps / 10 # Maybe even be 1, but not smaller
if (start_incr < 1):
start_incr = 1
# Initialisation
#
eps = beg_eps
i_small = -i_large
large_incr = int(i_large / 10)
thresh = min(int(num_rows / 5), 100) # Maximal value 100
incr_factor = 2
cycles = 1
average = num_cols
num_phases = 1
# Initialise dictionaries for prices and row assignments
#
pcol = {}
assigned = {}
for col_num in col_numbers:
pcol[col_num] = i_small
# assigned[col_num] = -1#######
# Initialise list of un-assigned rows (all rows at the beginning)
#
list = row_numbers[:]
no_list = num_rows
do_phase = True # Set flag so a first phase is performed
# Start sub problem (scaling phase with new epsilon) - - - - - - - - - - - -
#
while (do_phase == True):
if (eps == 1):
thresh = 0
incr = max(start_incr,
eps) # Increment must not be larger than epsilon
print '2: Start of a scaling phase with epsilon: %f' % (eps)
do_cycle = True # Set flag so a first cycle is performed
cycle_count = 0
while (do_cycle == True):
# Start forward auction cycle - - - - - - - - - - - - - - - - - - - - - -
#
no_new_list = 0 # Initialise count of next list of un-assigned rows
# Cycle through the current list of un-assigned rows
#
for i in range(no_list):
row_num = list[i]
row_dict = cost_dict[row_num]
row_list = row_dict.items()
row_list.sort() ################ Maybe not needed ??? #######
row_len = len(row_dict)
# Get first and second column number and cost
#
col_num, cost = row_list[0]
col_num2, cost2 = row_list[1]
max1 = cost - pcol[col_num]
max2 = cost2 - pcol[col_num2]
if (max1 > max2):
best_col_num = col_num
elif (max1 < max2): # Swap maximum values
max1, max2 = max2, max1
best_col_num = col_num2
else: # Both are the same
if (col_num < col_num2
): # Make sure best column number is smallest
best_col_num = col_num
else:
best_col_num = col_num2
if (row_len > 2): # Row has more than two elements
for c in range(2, row_len):
col_num3, cost3 = row_list[c] # Loop through cols
max_tmp = cost3 - pcol[col_num3]
if (max_tmp > max2):
if (max_tmp > max1):
best_col_num = col_num3 # New best column
max2 = max1
max1 = max_tmp
elif (max_tmp
== max1) and (col_num3 < best_col_num):
best_col_num = col_num3 # Best column number is smallest
else:
max2 = max_tmp
# Row bids for best column increasing its price, and gets - - - - - -
# assigned to best column, while any row assigned to best
# column gets un-asssigned
#
pcol[best_col_num] = pcol[best_col_num] + max1 - max2 + incr
old_row = assigned.get(best_col_num, -1) #########
assigned[best_col_num] = row_num
if (old_row >= 0): # Row has been assigned
list[
no_new_list] = old_row # Save un-assigned row into list
no_new_list += 1
cycle_count += 1
if ((cycle_count % 10000) == 0):
print '1: Finished %i cycles, %i out of %i rows un-assigned' % \
(cycle_count, no_new_list, num_rows)
if (no_new_list > 0):
print '1: Un-assigned rows: %s' % (str(
list[:no_new_list]))
# Collect statistics
#
average = (cycles * average + no_list) / (cycles + 1)
cycles += 1
# Check if there are still 'many' unassignedrows, i.e. if the - - - - - -
# number of unassignd rows is greater than the parameter 'thresh'.
# If not, replace current list with the new list and go for another
# cycle. Otherwise, if epsilon > 1, reduce epsilon, reset the
# asignment to empty and restart auction.
# If epsilon == 1 terminate.
# Also increase the minimal bidding increment up to a maximun value
# of epsilon (this is the adaptive feature)
#
incr *= incr_factor
if (incr > eps):
incr = eps
if (no_new_list > thresh):
no_list = no_new_list
else:
do_cycle = False # Set flag so cycle is left
# End of sub-problem (scaling phase) - - - - - - - - - - - - - - - - - - -
#
if (eps == 1):
do_phase = False # Set flag so phase is left
else:
num_phases += 1
eps = int(eps / factor)
if (eps > incr):
eps = int(eps / factor)
if (eps < 1) or (eps < end_eps):
eps = 1
thresh = int(thresh / factor)
print '1: End of a scaling phase, new epsilon: %3f' % (eps)
t_min = min(pcol.values() + [i_large])
col_num_list = assigned.keys() ##########
col_num_list.sort() ##########
for col_num in assigned: ###########
# for col_num in col_num_list:
row_num = assigned[col_num]
if (row_num >= 0):
list[no_new_list] = row_num
no_new_list += 1
assigned[col_num] = -1
incr = t_min - i_small # Reset minimum price to i_small
for col_num in col_numbers: # Update all prices
pcol[col_num] = pcol[col_num] - incr
# Final parameter updates before starting another scaling phase
#
no_list = no_new_list
if (start_incr < eps):
start_incr *= factor
return assigned
def do_lap(lap_method, results_dict, process_type, threshold):
"""Linear sum assignment procedure.
This routine calculates a linear assignments for one-to-one matching.
The routine do_lap does all kinds of preprocessing, including the
extraction of unique record pairs (which can be removed before the lap is
applied) and the extraction of sub-set which can be solved independently.
These sub-sets are then given to the chosen lap routine.
The routine takes as input a results dictionary, as produced by a
classifier (see classification.py), and returns a dictionary with the
assigned record pair numbers as keys and the corresponding weight as
values.
Possible methods are 'auction'
The process_type attribute must either be set to 'deduplication' or to
'linkage' in order to be able to preprocess the classifier data prior to
the lap procedure.
"""
if (lap_method not in ['auction']):
print 'error:Illegal method for lap method: %s' % (str(lap_method))
raise Exception
if (process_type not in ['deduplication', 'linkage']):
print 'error:Illegal value for attribute "process_type": %s' %\
(str(process_type))
raise Exception
if (results_dict == {}):
print 'error:Empty results dictionary'
raise Exception
lap_start_time = time.time() # Start timer
lap_results = {} # Result dictionary with final record pair matches
# Make one (or two) disctionary of all assigned rercord numbers
#
if (process_type == 'deduplication'):
used_rec_nums = {}
else:
used_rec_nums_a = {}
used_rec_nums_b = {}
# Make sure the threshold is a number if it is defined
#
if (threshold != None):
if (not (isinstance(threshold, int) or isinstance(threshold, float))):
print 'error:Threshold is not a number: %s' % (str(threshold))
raise Exception
print '1: Start linear assignment procedure using method: %s' % (
lap_method)
print '1: Original length of results dictionary: %i' % (
len(results_dict))
# Step 1: Filter out record pairs with weight lower than the threshold - - -
#
if (threshold != None):
print '1: Remove record pairs with weight less than: %f' % (
threshold)
else:
threshold = -999999999999.999 # Make it a very very small number
work_dict = {} # Make an empty working dictionary
for row_num in results_dict: # Loop over all record numbers (keys)
row_dict = results_dict[row_num] # Get corresponding record dictionary
new_row_dict = {} # Start a new record dictionary
for col_num in row_dict: # Loop over all records in this dictionary
weight = row_dict[col_num]
if (weight >= threshold):
new_row_dict[col_num] = weight # Copy to new dictionary
if (new_row_dict != {}): # Only insert non empty dictionaries
work_dict[row_num] = new_row_dict
results_len = len(work_dict) # Save results length (after filtering)
if (threshold > -999999999999.999):
print '1: Length of working dictionary after filtering: %i' % \
(results_len)
# Step 2: Remove all matches (record pairs) which are unique - - - - - - - -
# (i.e. which don't have matches with other records)
#
row_num_dict = {} # Count occurences of record numbers in rows
col_num_dict = {} # Count occurences of record numbers in columns
for row_num in work_dict: # First count occurences of rows and columns
# Insert a count for the row number
#
row_num_dict[row_num] = row_num_dict.get(row_num, 0) + 1
row_dict = work_dict[row_num]
for col_num in row_dict:
# Increase a count for a column number
#
col_num_dict[col_num] = col_num_dict.get(col_num, 0) + 1
if (process_type == 'deduplication'):
# For deduplication, insert symmetric record numbers as well
#
row_num_dict[col_num] = row_num_dict.get(col_num, 0) + 1
col_num_dict[row_num] = col_num_dict.get(row_num, 0) + 1
for row_num in work_dict.keys(): # Secondly remove unique rows and column
row_dict = work_dict[row_num] # Get corresponding record dictionary
if (len(row_dict) == 1): # Only one record pair for this record
col_num, weight = row_dict.items()[
0] # Get the only element in row
if (row_num_dict[row_num] == 1) and (col_num_dict[col_num] == 1):
#################### START TEST CODE ##################################
if (DO_TESTS == True):
if (process_type == 'deduplication'):
if (row_num in used_rec_nums):
print 'warning:Record number %i already used for deduplication' \
% (row_num)
if (col_num in used_rec_nums):
print 'warning:record number %i already used for deduplication' \
% (col_num)
else:
if (row_num in used_rec_nums_a):
print 'warning:Record number A %i already used for linkage' % \
(row_num)
if (col_num in used_rec_nums_b):
print 'warning:record number B %i already used for linkage' % \
(col_num)
#################### END TEST CODE ##################################
lap_results[(row_num,
col_num)] = True # Insert into final results
del work_dict[row_num] # And delete the record in the results
if (process_type == 'deduplication'):
used_rec_nums[row_num] = True
used_rec_nums[col_num] = True
else:
used_rec_nums_a[row_num] = True
used_rec_nums_b[col_num] = True
print '1: Found and extracted %i unique record ' % (len(lap_results)) + \
'pairs in results dictionary'
for rec_pair in lap_results:
print '3: %s' % (str(rec_pair))
print '3:'
lap_pair_extract_time = time.time() - lap_start_time
#################### START PARALLEL TEST CODE ###########################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = lap_results.items()
tmp_list.sort()
f = open('one2one-unique-dedup-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'w')
for c in tmp_list:
f.write(str(c) + os.linesep)
f.close()
tmp_list = work_dict.keys()
tmp_list.sort()
f = open(
'work-dict-' + str(parallel.rank()) + '-' + str(parallel.size()),
'w')
for c in tmp_list:
cc = work_dict[c].items()
cc.sort()
f.write(str(c) + ':: ' + str(cc) + os.linesep)
f.close()
#################### END PARALLEL TEST CODE #############################
#################### START TEST CODE ########################################
# Test if a record only appears once in the lap results dictionary
#
if (DO_TESTS == True):
if (process_type == 'deduplication'):
test_dict = {}
for (rec_a, rec_b) in lap_results:
if (test_dict.has_key(rec_a)):
print 'warning:Record %s is already in the test dictionary' % \
(str(rec_a))
else:
test_dict[rec_a] = 1
if (test_dict.has_key(rec_b)):
print 'warning:Record %s is already in the test dictionary' % \
(str(rec_b))
else:
test_dict[rec_b] = 1
else: # Linkage process
test_dict_a = {}
test_dict_b = {}
for (rec_a, rec_b) in lap_results:
if (test_dict_a.has_key(rec_a)):
print 'warning:Record %s is already in test dictionary A' % \
(str(rec_a))
else:
test_dict_a[rec_a] = 1
if (test_dict_b.has_key(rec_b)):
print 'warning:Record %s is already in test dictionary B' % \
(str(rec_b))
else:
test_dict_b[rec_b] = 1
#################### END TEST CODE ##########################################
if (len(work_dict) == 0
): # All record pairs are processed - - - - - - - - -
return lap_results
print '1: Remaining number of records in working dictionary: %i' % \
(len(work_dict)) + ' (down from: %i)' % (results_len)
# Step 3: Find connected sub-sets in the results dictionary - - - - - - - - -
# (using depth-first search)
#
visited = {} # Dictionary which will contain all so far visited rows
sub_sets = {} # Dictionary which will contain the sub-sets extracted
print '1: Find connected sub-graphs in results dictionary'
lap_subset_start_time = time.time()
max_sub_set_length = -1
num_visited = 0 # Number of rows visited so far
row_num_done = 0
work_dict_len = len(work_dict)
work_dict_rows = work_dict.keys()
work_dict_rows.sort()
# Create a column oriented work dictionary - - - - - - - - - - - - - - - - -
#
col_work_dict = {}
for row_num in work_dict_rows: # Loop over all rows
row_dict = work_dict[row_num]
for col_num in row_dict:
col_dict = col_work_dict.get(col_num, {})
col_dict[
row_num] = True # Only position is needed, but not the weight
col_work_dict[col_num] = col_dict
for row_num in work_dict_rows: # Loop over all rows
if (not visited.has_key(row_num)): # This row has not been visited yet
visited[row_num] = row_num # Mark visited as 'seeding' row
num_visited += 1
print '2: Create sub-set with seeding record %i' % (row_num)
process_queue = [row_num] # Start a new queue of rows to process
row_sub_set = {row_num: 1} # Row numbers connected to this row
while (process_queue !=
[]): # Process rows until all connected rows done
print '3: Process queue: %s' % (str(process_queue))
next_row = process_queue.pop(
0) # Get and remove first row to process
row_col_numbers = work_dict[next_row].keys(
) # Get columns in this row
# For deduplication, also insert row number into this column numbers
#
if (process_type == 'deduplication'):
row_col_numbers.append(next_row)
print '3: Row %i with column numbers: %s' % \
(next_row, str(row_col_numbers))
# Get the row numbers from all column numbers
#
for col_num in row_col_numbers:
# Get list of all row numbers in this column
#
row_num_dict = col_work_dict.get(col_num, {})
row_num_list = row_num_dict.keys()
if (process_type == 'deduplication') and (col_num in work_dict) and \
(col_num not in row_num_list):
row_num_list.append(col_num)
print '3: Column: %i with row numbers: %s' % \
(col_num, str(row_num_list))
for row_num2 in row_num_list:
row_sub_set[row_num2] = 1
if (not visited.has_key(row_num2)
): # Check if it's a new row
process_queue.append(row_num2)
print '3: Appended row number %i to process queue' % \
(row_num2)
visited[
row_num2] = row_num # Mark row as visited by seeding row
num_visited += 1
print '3: Row %i connected to row %i' % \
(row_num2, row_num)
sub_sets[row_num] = row_sub_set.keys() # Only store keys
if (len(row_sub_set) > max_sub_set_length):
max_sub_set_length = len(row_sub_set)
print '3: Sub-set contains records: %s' % \
(str(row_sub_set.keys()))
row_num_done += 1
# Now determine timing and print progress report (every 10%) - - - - - - -
# (only if more than 100 records in the work dictionary)
#
if (work_dict_len >= 100) and (row_num_done % int(work_dict_len / 10)
== 0):
used_time = time.time() - lap_subset_start_time
perc_done = 100.0 * row_num_done / work_dict_len
# todo_time = (work_dict_len - row_num_done) * \ #################
# (used_time / row_num_done)
todo_time = (work_dict_len - num_visited) * \
(used_time / row_num_done)
used_time_string = output.time_string(used_time)
todo_time_string = output.time_string(todo_time)
print '1: Processed %.1f%% of records in %s (%i/%i records ' % \
(perc_done, used_time_string, num_visited, work_dict_len) + \
'visited)'
print '1: Estimated %s until finished' % (todo_time_string)
del col_work_dict # Delete the column oriented work dictionary
num_sub_sets = len(sub_sets) # Get the total number of sub-sets
lap_subset_total_time = time.time() - lap_subset_start_time
lap_subset_total_time_string = output.time_string(lap_subset_total_time)
print '1: Extracted %i sub-sets in %s' % \
(num_sub_sets, lap_subset_total_time_string)
print '1: Longest sub-set contains %i rows' % (max_sub_set_length)
#################### START TEST CODE ########################################
# Test if all the sub-sets are mutually exclusive, and if the seed rows are
# in the sub-set record lists
#
if (DO_TESTS == True):
for seed_row in sub_sets:
row_list = sub_sets[seed_row]
if (seed_row not in row_list):
print 'warning:Seed row %s not in sub-set row list: %s' % \
(str(seed_rec), str(row_list))
for rec_num in row_list:
for seed_row2 in sub_sets:
row_list2 = sub_sets[seed_row2]
if (seed_row != seed_row2): # Don't test itself
if (rec_num in row_list2):
print 'warning:Record %s in more than one sub-set: %s, %s' % \
(str(rec_num), str(row_list), str(row_list2))
#################### END TEST CODE ##########################################
#################### START PARALLEL TEST CODE ###########################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = sub_sets.keys()
tmp_list.sort()
f = open('sub-sets-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'w')
for s in tmp_list:
tmp_sub_set = sub_sets[s]
tmp_sub_set.sort()
f.write(str(s) + '::' + str(tmp_sub_set) + os.linesep)
f.close()
#################### END PARALLEL TEST CODE #############################
# Now loop over all sub-sets - - - - - - - - - - - - - - - - - - - - - - - -
# (pre-process them first before giving them to the actual linear assignment
# method)
#
lap_lap_start_time = time.time()
lap_comm_time = 0.0
sub_set_cnt = 0 # A round robin counter, used for parallelism
sub_set_rows = sub_sets.keys()
sub_set_rows.sort() # Needed to make the same on all processes
for seed_row in sub_set_rows:
# Distribute sub-sets equally to all processors
#
if ((sub_set_cnt % parallel.size()) == parallel.rank()):
row_list = sub_sets[seed_row]
row_list.sort()
print '1:'
print '1: Sub-set %i of %i with seed row %i contains %i rows' % \
(sub_set_cnt, num_sub_sets, seed_row, len(row_list))
print '3: Sub-set rows: %s' % (str(row_list))
if (len(row_list) == 1
): # Special case: One row only - - - - - - - - -
max_weight = -99999.9
max_col = -1
row_dict = work_dict[
row_list[0]] # Get the dictionary for this row
# Find element with largest weight
#
for col_num in row_dict:
weight = row_dict[col_num]
if (weight > max_weight):
max_weight = weight
max_col = col_num
# Assignment dictionary is of form col_num:row_num
#
tmp_assign_dict = {
max_col: row_list[0]
} # Make record pair dictionary
print '2: Special case sub-set with one row only, ' + \
'assignment pair: (%i,%i)' % (row_list[0], max_col)
else: # General case with more than one row - - - - - - - - - - - - - -
# Get minimal and maximal weights, and lists with row and column
# numbers
#
min_weight = 999999.9
max_weight = -999999.9
col_numbers = {}
row_col_numbers = {}
for row_num in row_list: # Loop over rows in this sub-set
row_dict = work_dict[
row_num] # Get the dictionary for this row
row_col_numbers[row_num] = 1
for col_num in row_dict:
weight = row_dict[col_num]
col_numbers[col_num] = 1
row_col_numbers[col_num] = 1
if (weight < min_weight):
min_weight = weight
if (weight > max_weight):
max_weight = weight
print '3: Minimal and maximal weight: %.3f / %.3f' % \
(min_weight, max_weight)
row_numbers = work_dict.keys()
col_numbers = col_numbers.keys()
row_numbers.sort()
col_numbers.sort()
num_rows = len(row_numbers)
num_cols = len(col_numbers)
row_col_numbers = row_col_numbers.keys()
row_col_numbers.sort()
#print '1: Row numbers: %s' % (str(row_numbers))
#print '1: Column numbers: %s' % (str(col_numbers))
#print '1: Row/colum numbers: %s' % (str(row_col_numbers))
#print '1: Number of unique weights: %i' % (len(weight_dict))
# Deal with the special case that there is only one column number - - -
#
if (num_cols == 1):
max_weight = -99999.9
max_row = -1
col_num = col_numbers[0] # Get the column number
# Find element with largest weight
#
for row_num in row_list: # Loop over rows
# Get only weight in row
#
row_weight = work_dict[row_num].values()[0]
if (row_weight > max_weight):
max_weight = row_weight
max_row = row_num
# Assignment dictionary is of form col_num:row_num
#
tmp_assign_dict = {
col_num: max_row
} # Make record pair dictionary
print '2: Special case sub-set with one column only, ' + \
'assignment pair: (%i,%i)' % (max_row, col_num)
else: # General case with more than one row and column - - - - - - - -
# Construct the cost dictionary - - - - - - - - - - - - - - - - - - -
#
cost_dict = {}
dim = len(row_col_numbers) # Final dimension of the LAP
min_cost = -max_weight * (dim + 1) # Use original wieghts
for row_num in row_list: # Loop over rows
row_dict = work_dict[row_num]
# Get the column numbers in this row
#
col_list = row_dict.keys()
col_list.sort()
row_cost_dict = cost_dict.get(row_num, {})
for col_num in col_list:
weight = row_dict[col_num]
cost = weight * (dim + 1) # Use original weights
row_cost_dict[
col_num] = cost # And store into row dictionary
# Insert symmetric element as well (if not on diagonal)
#
if (row_num != col_num):
row_cost_dict2 = cost_dict.get(col_num, {})
if (row_num not in row_cost_dict2
): # Only insert if not there
if (process_type == 'deduplication'):
row_cost_dict2[
row_num] = cost # Insert symmetric cost
else: # Linkage process
row_cost_dict2[
row_num] = min_cost # Insert minimal cost
# And insert diagonal element if there is none
#
if (not row_cost_dict2.has_key(col_num)):
row_cost_dict2[col_num] = min_cost
cost_dict[col_num] = row_cost_dict2
# Make sure there is a diagonal element (for feasibility)
#
if (not row_cost_dict.has_key(row_num)):
row_cost_dict[row_num] = min_cost
# If more than MAX_ROW_ELEMENTS elements in row only take the
# largest (following an idea by William Winkler)
#
if (len(row_cost_dict) > MAX_ROW_ELEMENTS):
row_col_numbers = row_cost_dict.keys()
row_weights = row_cost_dict.values()
row_elem_list = map(None, row_weights,
row_col_numbers)
row_elem_list.sort()
diag_weight = row_cost_dict[
row_num] # Keep diagonal element
row_cost_dict = {row_num: diag_weight}
##print ' '
##print '****** row_elem_list: %s' % (str(row_elem_list))
##print ' '
for (weight,
col_num) in row_elem_list[-MAX_ROW_ELEMENTS:]:
row_cost_dict[col_num] = weight
# Insert row into cost dictionary
#
cost_dict[row_num] = row_cost_dict
# Get the final row and column numbers - - - - - - - - - - - - - - -
#
row_numbers = cost_dict.keys()
col_numbers = {}
for row_dict in cost_dict.values():
col_numbers.update(row_dict)
col_numbers = col_numbers.keys()
row_numbers.sort()
col_numbers.sort()
# Check if number of rows and columns are equal - - - - - - - - - - -
#
if (len(row_numbers) != len(col_numbers)):
print 'error:Different number of rows (%i) and columns (%i)' \
% (len(row_numbers), len(col_numbers))
raise Exception
print '1: Cost dictionary with %i rows/columns given to ' % \
(len(row_numbers)) + 'assignment method %s:' % (lap_method)
print '2: Row numbers: %s' % (str(row_numbers))
print '2: Column numbers: %s' % (str(row_numbers))
print '2: Minimal weight: %3f' % (min_weight)
print '2: Maximal weight: %3f' % (max_weight)
print '3: Cost dictionary: %s' % (str(cost_dict))
print '3: Process type: %s' % (process_type)
#################### START PARALLEL TEST CODE #######################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = cost_dict.keys()
tmp_list.sort()
tmp_str = str(sub_set_cnt)+':: '+ str(min_weight) + ' / ' + \
str(max_weight) + ', ' + str(row_numbers) + ', ' + \
process_type + '::'
for k in tmp_list:
tmp_list2 = cost_dict[k].items()
tmp_list2.sort()
tmp_str = tmp_str + ' ' + str(tmp_list2) + ' / '
f = open('lap-calling-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'a')
f.write(tmp_str + os.linesep)
f.close()
#################### END PARALLEL TEST CODE #########################
# Call the lap method which returns an assignment dictionary - - - -
#
if (lap_method == 'auction'):
tmp_assign_dict = auction(cost_dict, min_weight, max_weight, \
row_numbers, col_numbers)
else:
print 'error:LAP method %s not implemented' % (
lap_method)
raise Exception
# If run in parallel, send temporary assignment dictionary process 0 - -
#
if (parallel.rank() > 0):
tmp_time = time.time()
parallel.send(tmp_assign_dict, 0)
lap_comm_time += (time.time() - tmp_time)
print '1: Sent assignment dictionary with %i entries to process' \
% (len(tmp_assign_dict)) + ' 0'
# Only process 0 inserts temporary assignment dictionary into results - - -
#
if (parallel.rank() == 0):
# Receive assignment dictionary from other process if necessary
#
p = (sub_set_cnt % parallel.size()
) # Process number to receive from
if (p != 0):
tmp_time = time.time()
tmp_assign_dict = parallel.receive(p)
lap_comm_time += (time.time() - tmp_time)
print '1: Received subset %i of %i assignment dictionary with ' % \
(sub_set_cnt, num_sub_sets) + '%i entries from process %i' % \
(len(tmp_assign_dict), p)
# Post-process the assignment dictionary - - - - - - - - - - - - - - - -
#
assign_pairs = {}
for rec_num_b in tmp_assign_dict:
rec_num_a = tmp_assign_dict[rec_num_b]
# Now check if this record pair is in the original results dictionary
#
if (rec_num_a in results_dict):
row_dict = results_dict[rec_num_a]
if (rec_num_b in row_dict):
weight = row_dict[rec_num_b]
# Insert into dictionary of potential record pairs
#
assign_pairs[(rec_num_a, rec_num_b)] = weight
#################### START PARALLEL TEST CODE ###########################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = tmp_assign_dict.items()
tmp_list.sort()
tmp_list2 = assign_pairs.items()
tmp_list2.sort()
tmp_list3 = sub_sets[seed_row]
tmp_list3.sort()
f = open('assignments-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'a')
f.write(str(sub_set_cnt) + ', ' + str(seed_row) + os.linesep)
f.write(str(tmp_list) + os.linesep)
f.write(str(tmp_list2) + os.linesep)
f.write(str(tmp_list3) + os.linesep)
f.write(os.linesep)
f.close()
#################### END PARALLEL TEST CODE #############################
# Sort the assigned pairs according to their weight
#
assign_weights = assign_pairs.values() # Get the weights in a list
assign_rec_pairs = assign_pairs.keys() # And the record pairs
assign_pair_list = map(None, assign_weights, assign_rec_pairs)
assign_pair_list.sort()
num_assigned_pairs = 0 # Number of assigned pairs for this sub-set
dedup_check_rec_nums = {} # Already assigned record numbers
while (assign_pair_list != []): # Now check all record pairs
check_pair = assign_pair_list.pop(
) # Get largest weight record pair
weight = check_pair[0]
rec_num_a = check_pair[1][0]
rec_num_b = check_pair[1][1]
rec_pair = (rec_num_a, rec_num_b)
# Now check if a record pair has already been used in an assignment
# and for a deduplication process also check if any of the two
# records has been used in an assignment
#
if ((process_type == 'linkage') and \
(rec_num_a not in used_rec_nums_a) and \
(rec_num_b not in used_rec_nums_b)) or \
((process_type == 'deduplication') and \
(rec_num_a not in used_rec_nums) and \
(rec_num_b not in used_rec_nums)):
# For deduplication insert record numbers into used record numbers
#
if (process_type == 'deduplication'):
used_rec_nums[rec_num_a] = True
used_rec_nums[rec_num_b] = True
else:
used_rec_nums_a[rec_num_a] = True
used_rec_nums_b[rec_num_b] = True
if (rec_pair not in lap_results):
lap_results[rec_pair] = True
num_assigned_pairs += 1
else:
print 'warning:Record pair (%i,%i) already in LAP results' \
% (rec_num_a, rec_num_b)
print '2: Inserted %i (out of %i) record pairs into LAP ' % \
(num_assigned_pairs, len(tmp_assign_dict)) + 'results'
sub_set_cnt += 1
# Report progress every 10% (only if more than 100 sub-sets) - - - - - - -
#
if (num_sub_sets >= 100) and (sub_set_cnt % int(num_sub_sets / 10)
== 0):
used_time = time.time() - lap_lap_start_time
perc_done = 100.0 * sub_set_cnt / num_sub_sets
sub_set_time = used_time / sub_set_cnt
todo_time = (num_sub_sets - sub_set_cnt) * sub_set_time
used_time_string = output.time_string(used_time)
todo_time_string = output.time_string(todo_time)
sub_set_time_string = output.time_string(sub_set_time)
print '1: Processed %.1f%% (%i/%i) of sub-sets in %s' % \
(perc_done, sub_set_cnt, num_sub_sets, used_time_string) + \
' (%s per sub-set)' % (sub_set_time_string)
print '1: Estimated %s until finished' % (todo_time_string)
print '1: Total number of assignments: %i' % (len(lap_results))
print '1: Number of rows in original results dictionary: %i' % \
(len(results_dict))
#################### START TEST CODE ########################################
# Test if a record only appears once in the lap results dictionary
#
if (DO_TESTS == True) and (parallel.rank() == 0):
if (process_type == 'deduplication'):
test_dict = {}
for (rec_a, rec_b) in lap_results:
if (test_dict.has_key(rec_a)):
print 'warning:Record %i is already in the test dictionary' % \
(rec_a)+' rec_pair: (%i,%i)' % (rec_a, rec_b)
else:
test_dict[rec_a] = True
if (test_dict.has_key(rec_b)):
print 'warning:Record %i is already in the test dictionary' % \
(rec_b)+' rec_pair: (%i,%i)' % (rec_a, rec_b)
else:
test_dict[rec_b] = 1
else: # Linkage process
test_dict_a = {}
test_dict_b = {}
for (rec_a, rec_b) in lap_results:
if (test_dict_a.has_key(rec_a)):
print 'warning:Record %s is already in test dictionary A' % \
(str(rec_a))
else:
test_dict_a[rec_a] = 1
if (test_dict_b.has_key(rec_b)):
print 'warning:Record %s is already in test dictionary B' % \
(str(rec_b))
else:
test_dict_b[rec_b] = 1
#################### END TEST CODE ##########################################
lap_stop_time = time.time()
lap_lap_time = lap_stop_time - lap_lap_start_time
lap_total_time = lap_stop_time - lap_start_time
lap_pair_extract_time_string = output.time_string(lap_pair_extract_time)
lap_subset_total_time_string = output.time_string(lap_subset_total_time)
lap_lap_time_string = output.time_string(lap_lap_time)
if (parallel.size() > 1):
lap_comm_time_string = output.time_string(lap_comm_time)
lap_total_time_string = output.time_string(lap_total_time)
print '1:'
print '1: Finished linear record pair assignment procedure'
print '1: Time for extracting unique record pairs: %s' % \
(lap_pair_extract_time_string)
print '1: Time for creating record sub-sets: %s' % \
(lap_subset_total_time_string)
print '1: Time for linear assignment algorithm: %s' % \
(lap_lap_time_string)
if (parallel.size() > 1):
print '1: Time for communication: %s' % \
(lap_comm_time_string)
print '1: Total time for linear assignment: %s' % \
(lap_total_time_string)
print '1:'
return lap_results
def auction(cost_dict, min_cost, max_cost, row_numbers, col_numbers):
"""Linear sum assignment procedure based on symetric auction algorithm.
Re-implementation of a FORTRAN code, taken from:
http://web.mit.edu/afs/athena.mit.edu/user/d/i/dimitrib/www/auction.txt
and as described in:
"Auction Algorithms for Network Flow Problems: A Tutorial Introduction"
Dimitri P. Bertsekas, Computational Optimization and Applications, Vol.
1, pp. 7-66, 1992.
and other papers by Dimitri P. Bertsekas, see:
http://www.mit.edu:8001//people/dimitrib/publ.html
Takes as input a cost dictionary, the minimum and maximum weights in this
dictionary, and two sorted lists with the row and column numbers.
"""
#################### START PARALLEL TEST CODE ###############################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = cost_dict.keys()
tmp_list.sort()
tmp_str = str(min_cost) + ' /' + str(max_cost)+', '+ str(row_numbers) + \
' / ' + str(col_numbers) + ':: '
for k in tmp_list:
tmp_list2 = cost_dict[k].items()
tmp_list2.sort()
tmp_str = tmp_str + ' ' + str(tmp_list2) + ' / '
f = open('lap-auction-'+str(parallel.rank())+'-'+str(parallel.size()),'a')
f.write(tmp_str+os.linesep)
f.close()
#################### END PARALLEL TEST CODE ###############################
i_large = 100000000 # A value larger than max_cost
auction_results = {} # Result dictionary with final record pair matches
num_rows = len(row_numbers)
num_cols = len(col_numbers)
if (num_rows != num_cols):
print 'error:Asymmetric problem given to symmetric "auction" algorithm'
raise Exception
# Set parameters for auction algorithm - - - - - - - - - - - - - - - - - - -
#
if (max_cost > int(i_large / (num_rows + 1))):
print 'error:Cost range too large to work with integer epsilon'
raise Exception
max_cost *= (num_rows + 1)
beg_eps = max_cost / 5 # Maybe smaller, can even be 1, but not smaller
end_eps = num_rows / 10 # Must be smaller than beg_eps, can be 1
if (end_eps < 1):
end_eps = 1
elif (end_eps > beg_eps):
end_eps = beg_eps
factor = 5 # Must be greater than 1
start_incr = beg_eps / 10 # Maybe even be 1, but not smaller
if (start_incr < 1):
start_incr = 1
# Initialisation
#
eps = beg_eps
i_small = -i_large
large_incr = int(i_large / 10)
thresh = min(int(num_rows / 5), 100) # Maximal value 100
incr_factor = 2
cycles = 1
average = num_cols
num_phases = 1
# Initialise dictionaries for prices and row assignments
#
pcol = {}
assigned = {}
for col_num in col_numbers:
pcol[col_num] = i_small
# assigned[col_num] = -1#######
# Initialise list of un-assigned rows (all rows at the beginning)
#
list = row_numbers[:]
no_list = num_rows
do_phase = True # Set flag so a first phase is performed
# Start sub problem (scaling phase with new epsilon) - - - - - - - - - - - -
#
while (do_phase == True):
if (eps == 1):
thresh = 0
incr = max(start_incr, eps) # Increment must not be larger than epsilon
print '2: Start of a scaling phase with epsilon: %f' % (eps)
do_cycle = True # Set flag so a first cycle is performed
cycle_count = 0
while (do_cycle == True):
# Start forward auction cycle - - - - - - - - - - - - - - - - - - - - - -
#
no_new_list = 0 # Initialise count of next list of un-assigned rows
# Cycle through the current list of un-assigned rows
#
for i in range(no_list):
row_num = list[i]
row_dict = cost_dict[row_num]
row_list = row_dict.items()
row_list.sort() ################ Maybe not needed ??? #######
row_len = len(row_dict)
# Get first and second column number and cost
#
col_num, cost = row_list[0]
col_num2, cost2 = row_list[1]
max1 = cost - pcol[col_num]
max2 = cost2 - pcol[col_num2]
if (max1 > max2):
best_col_num = col_num
elif (max1 < max2): # Swap maximum values
max1, max2 = max2, max1
best_col_num = col_num2
else: # Both are the same
if (col_num < col_num2): # Make sure best column number is smallest
best_col_num = col_num
else:
best_col_num = col_num2
if (row_len > 2): # Row has more than two elements
for c in range(2, row_len):
col_num3, cost3 = row_list[c] # Loop through cols
max_tmp = cost3 - pcol[col_num3]
if (max_tmp > max2):
if (max_tmp > max1):
best_col_num = col_num3 # New best column
max2 = max1
max1 = max_tmp
elif (max_tmp == max1) and (col_num3 < best_col_num):
best_col_num = col_num3 # Best column number is smallest
else:
max2 = max_tmp
# Row bids for best column increasing its price, and gets - - - - - -
# assigned to best column, while any row assigned to best
# column gets un-asssigned
#
pcol[best_col_num] = pcol[best_col_num] + max1 - max2 + incr
old_row = assigned.get(best_col_num, -1) #########
assigned[best_col_num] = row_num
if (old_row >= 0): # Row has been assigned
list[no_new_list] = old_row # Save un-assigned row into list
no_new_list += 1
cycle_count += 1
if ((cycle_count % 10000) == 0):
print '1: Finished %i cycles, %i out of %i rows un-assigned' % \
(cycle_count, no_new_list, num_rows)
if (no_new_list > 0):
print '1: Un-assigned rows: %s' % (str(list[:no_new_list]))
# Collect statistics
#
average = (cycles * average + no_list) / (cycles+1)
cycles += 1
# Check if there are still 'many' unassignedrows, i.e. if the - - - - - -
# number of unassignd rows is greater than the parameter 'thresh'.
# If not, replace current list with the new list and go for another
# cycle. Otherwise, if epsilon > 1, reduce epsilon, reset the
# asignment to empty and restart auction.
# If epsilon == 1 terminate.
# Also increase the minimal bidding increment up to a maximun value
# of epsilon (this is the adaptive feature)
#
incr *= incr_factor
if (incr > eps):
incr = eps
if (no_new_list > thresh):
no_list = no_new_list
else:
do_cycle = False # Set flag so cycle is left
# End of sub-problem (scaling phase) - - - - - - - - - - - - - - - - - - -
#
if (eps == 1):
do_phase = False # Set flag so phase is left
else:
num_phases += 1
eps = int(eps / factor)
if (eps > incr):
eps = int(eps / factor)
if (eps < 1) or (eps < end_eps):
eps = 1
thresh = int(thresh / factor)
print '1: End of a scaling phase, new epsilon: %3f' % (eps)
t_min = min(pcol.values()+[i_large])
col_num_list = assigned.keys() ##########
col_num_list.sort() ##########
for col_num in assigned: ###########
# for col_num in col_num_list:
row_num = assigned[col_num]
if (row_num >= 0):
list[no_new_list] = row_num
no_new_list += 1
assigned[col_num] = -1
incr = t_min - i_small # Reset minimum price to i_small
for col_num in col_numbers: # Update all prices
pcol[col_num] = pcol[col_num] - incr
# Final parameter updates before starting another scaling phase
#
no_list = no_new_list
if (start_incr < eps):
start_incr *= factor
return assigned
def do_lap(lap_method, results_dict, process_type, threshold):
"""Linear sum assignment procedure.
This routine calculates a linear assignments for one-to-one matching.
The routine do_lap does all kinds of preprocessing, including the
extraction of unique record pairs (which can be removed before the lap is
applied) and the extraction of sub-set which can be solved independently.
These sub-sets are then given to the chosen lap routine.
The routine takes as input a results dictionary, as produced by a
classifier (see classification.py), and returns a dictionary with the
assigned record pair numbers as keys and the corresponding weight as
values.
Possible methods are 'auction'
The process_type attribute must either be set to 'deduplication' or to
'linkage' in order to be able to preprocess the classifier data prior to
the lap procedure.
"""
if (lap_method not in ['auction']):
print 'error:Illegal method for lap method: %s' % (str(lap_method))
raise Exception
if (process_type not in ['deduplication', 'linkage']):
print 'error:Illegal value for attribute "process_type": %s' %\
(str(process_type))
raise Exception
if (results_dict == {}):
print 'error:Empty results dictionary'
raise Exception
lap_start_time = time.time() # Start timer
lap_results = {} # Result dictionary with final record pair matches
# Make one (or two) disctionary of all assigned rercord numbers
#
if (process_type == 'deduplication'):
used_rec_nums = {}
else:
used_rec_nums_a = {}
used_rec_nums_b = {}
# Make sure the threshold is a number if it is defined
#
if (threshold != None):
if (not (isinstance(threshold, int) or isinstance(threshold, float))):
print 'error:Threshold is not a number: %s' % (str(threshold))
raise Exception
print '1: Start linear assignment procedure using method: %s' % (lap_method)
print '1: Original length of results dictionary: %i' % (len(results_dict))
# Step 1: Filter out record pairs with weight lower than the threshold - - -
#
if (threshold != None):
print '1: Remove record pairs with weight less than: %f' % (threshold)
else:
threshold = -999999999999.999 # Make it a very very small number
work_dict = {} # Make an empty working dictionary
for row_num in results_dict: # Loop over all record numbers (keys)
row_dict = results_dict[row_num] # Get corresponding record dictionary
new_row_dict = {} # Start a new record dictionary
for col_num in row_dict: # Loop over all records in this dictionary
weight = row_dict[col_num]
if (weight >= threshold):
new_row_dict[col_num] = weight # Copy to new dictionary
if (new_row_dict != {}): # Only insert non empty dictionaries
work_dict[row_num] = new_row_dict
results_len = len(work_dict) # Save results length (after filtering)
if (threshold > -999999999999.999):
print '1: Length of working dictionary after filtering: %i' % \
(results_len)
# Step 2: Remove all matches (record pairs) which are unique - - - - - - - -
# (i.e. which don't have matches with other records)
#
row_num_dict = {} # Count occurences of record numbers in rows
col_num_dict = {} # Count occurences of record numbers in columns
for row_num in work_dict: # First count occurences of rows and columns
# Insert a count for the row number
#
row_num_dict[row_num] = row_num_dict.get(row_num, 0) + 1
row_dict = work_dict[row_num]
for col_num in row_dict:
# Increase a count for a column number
#
col_num_dict[col_num] = col_num_dict.get(col_num, 0) + 1
if (process_type == 'deduplication'):
# For deduplication, insert symmetric record numbers as well
#
row_num_dict[col_num] = row_num_dict.get(col_num, 0) + 1
col_num_dict[row_num] = col_num_dict.get(row_num, 0) + 1
for row_num in work_dict.keys(): # Secondly remove unique rows and column
row_dict = work_dict[row_num] # Get corresponding record dictionary
if (len(row_dict) == 1): # Only one record pair for this record
col_num, weight = row_dict.items()[0] # Get the only element in row
if (row_num_dict[row_num] == 1) and (col_num_dict[col_num] == 1):
#################### START TEST CODE ##################################
if (DO_TESTS == True):
if (process_type == 'deduplication'):
if (row_num in used_rec_nums):
print 'warning:Record number %i already used for deduplication' \
% (row_num)
if (col_num in used_rec_nums):
print 'warning:record number %i already used for deduplication' \
% (col_num)
else:
if (row_num in used_rec_nums_a):
print 'warning:Record number A %i already used for linkage' % \
(row_num)
if (col_num in used_rec_nums_b):
print 'warning:record number B %i already used for linkage' % \
(col_num)
#################### END TEST CODE ##################################
lap_results[(row_num,col_num)] = True # Insert into final results
del work_dict[row_num] # And delete the record in the results
if (process_type == 'deduplication'):
used_rec_nums[row_num] = True
used_rec_nums[col_num] = True
else:
used_rec_nums_a[row_num] = True
used_rec_nums_b[col_num] = True
print '1: Found and extracted %i unique record ' % (len(lap_results)) + \
'pairs in results dictionary'
for rec_pair in lap_results:
print '3: %s' % (str(rec_pair))
print '3:'
lap_pair_extract_time = time.time() - lap_start_time
#################### START PARALLEL TEST CODE ###########################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = lap_results.items()
tmp_list.sort()
f = open('one2one-unique-dedup-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'w')
for c in tmp_list:
f.write(str(c)+os.linesep)
f.close()
tmp_list = work_dict.keys()
tmp_list.sort()
f = open('work-dict-'+str(parallel.rank())+'-'+str(parallel.size()),'w')
for c in tmp_list:
cc = work_dict[c].items()
cc.sort()
f.write(str(c)+':: '+str(cc)+os.linesep)
f.close()
#################### END PARALLEL TEST CODE #############################
#################### START TEST CODE ########################################
# Test if a record only appears once in the lap results dictionary
#
if (DO_TESTS == True):
if (process_type == 'deduplication'):
test_dict = {}
for (rec_a, rec_b) in lap_results:
if (test_dict.has_key(rec_a)):
print 'warning:Record %s is already in the test dictionary' % \
(str(rec_a))
else:
test_dict[rec_a] = 1
if (test_dict.has_key(rec_b)):
print 'warning:Record %s is already in the test dictionary' % \
(str(rec_b))
else:
test_dict[rec_b] = 1
else: # Linkage process
test_dict_a = {}
test_dict_b = {}
for (rec_a, rec_b) in lap_results:
if (test_dict_a.has_key(rec_a)):
print 'warning:Record %s is already in test dictionary A' % \
(str(rec_a))
else:
test_dict_a[rec_a] = 1
if (test_dict_b.has_key(rec_b)):
print 'warning:Record %s is already in test dictionary B' % \
(str(rec_b))
else:
test_dict_b[rec_b] = 1
#################### END TEST CODE ##########################################
if (len(work_dict) == 0): # All record pairs are processed - - - - - - - - -
return lap_results
print '1: Remaining number of records in working dictionary: %i' % \
(len(work_dict)) + ' (down from: %i)' % (results_len)
# Step 3: Find connected sub-sets in the results dictionary - - - - - - - - -
# (using depth-first search)
#
visited = {} # Dictionary which will contain all so far visited rows
sub_sets = {} # Dictionary which will contain the sub-sets extracted
print '1: Find connected sub-graphs in results dictionary'
lap_subset_start_time = time.time()
max_sub_set_length = -1
num_visited = 0 # Number of rows visited so far
row_num_done = 0
work_dict_len = len(work_dict)
work_dict_rows = work_dict.keys()
work_dict_rows.sort()
# Create a column oriented work dictionary - - - - - - - - - - - - - - - - -
#
col_work_dict = {}
for row_num in work_dict_rows: # Loop over all rows
row_dict = work_dict[row_num]
for col_num in row_dict:
col_dict = col_work_dict.get(col_num,{})
col_dict[row_num] = True # Only position is needed, but not the weight
col_work_dict[col_num] = col_dict
for row_num in work_dict_rows: # Loop over all rows
if (not visited.has_key(row_num)): # This row has not been visited yet
visited[row_num] = row_num # Mark visited as 'seeding' row
num_visited += 1
print '2: Create sub-set with seeding record %i' % (row_num)
process_queue = [row_num] # Start a new queue of rows to process
row_sub_set = {row_num:1} # Row numbers connected to this row
while (process_queue != []): # Process rows until all connected rows done
print '3: Process queue: %s' % (str(process_queue))
next_row = process_queue.pop(0) # Get and remove first row to process
row_col_numbers = work_dict[next_row].keys() # Get columns in this row
# For deduplication, also insert row number into this column numbers
#
if (process_type == 'deduplication'):
row_col_numbers.append(next_row)
print '3: Row %i with column numbers: %s' % \
(next_row, str(row_col_numbers))
# Get the row numbers from all column numbers
#
for col_num in row_col_numbers:
# Get list of all row numbers in this column
#
row_num_dict = col_work_dict.get(col_num, {})
row_num_list = row_num_dict.keys()
if (process_type == 'deduplication') and (col_num in work_dict) and \
(col_num not in row_num_list):
row_num_list.append(col_num)
print '3: Column: %i with row numbers: %s' % \
(col_num, str(row_num_list))
for row_num2 in row_num_list:
row_sub_set[row_num2] = 1
if (not visited.has_key(row_num2)): # Check if it's a new row
process_queue.append(row_num2)
print '3: Appended row number %i to process queue' % \
(row_num2)
visited[row_num2] = row_num # Mark row as visited by seeding row
num_visited += 1
print '3: Row %i connected to row %i' % \
(row_num2, row_num)
sub_sets[row_num] = row_sub_set.keys() # Only store keys
if (len(row_sub_set) > max_sub_set_length):
max_sub_set_length = len(row_sub_set)
print '3: Sub-set contains records: %s' % \
(str(row_sub_set.keys()))
row_num_done += 1
# Now determine timing and print progress report (every 10%) - - - - - - -
# (only if more than 100 records in the work dictionary)
#
if (work_dict_len >= 100) and (row_num_done % int(work_dict_len/10) == 0):
used_time = time.time() - lap_subset_start_time
perc_done = 100.0 * row_num_done / work_dict_len
# todo_time = (work_dict_len - row_num_done) * \ #################
# (used_time / row_num_done)
todo_time = (work_dict_len - num_visited) * \
(used_time / row_num_done)
used_time_string = output.time_string(used_time)
todo_time_string = output.time_string(todo_time)
print '1: Processed %.1f%% of records in %s (%i/%i records ' % \
(perc_done, used_time_string, num_visited, work_dict_len) + \
'visited)'
print '1: Estimated %s until finished' % (todo_time_string)
del col_work_dict # Delete the column oriented work dictionary
num_sub_sets = len(sub_sets) # Get the total number of sub-sets
lap_subset_total_time = time.time() - lap_subset_start_time
lap_subset_total_time_string = output.time_string(lap_subset_total_time)
print '1: Extracted %i sub-sets in %s' % \
(num_sub_sets, lap_subset_total_time_string)
print '1: Longest sub-set contains %i rows' % (max_sub_set_length)
#################### START TEST CODE ########################################
# Test if all the sub-sets are mutually exclusive, and if the seed rows are
# in the sub-set record lists
#
if (DO_TESTS == True):
for seed_row in sub_sets:
row_list = sub_sets[seed_row]
if (seed_row not in row_list):
print 'warning:Seed row %s not in sub-set row list: %s' % \
(str(seed_rec), str(row_list))
for rec_num in row_list:
for seed_row2 in sub_sets:
row_list2 = sub_sets[seed_row2]
if (seed_row != seed_row2): # Don't test itself
if (rec_num in row_list2):
print 'warning:Record %s in more than one sub-set: %s, %s' % \
(str(rec_num), str(row_list), str(row_list2))
#################### END TEST CODE ##########################################
#################### START PARALLEL TEST CODE ###########################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = sub_sets.keys()
tmp_list.sort()
f = open('sub-sets-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'w')
for s in tmp_list:
tmp_sub_set = sub_sets[s]
tmp_sub_set.sort()
f.write(str(s)+'::'+str(tmp_sub_set)+os.linesep)
f.close()
#################### END PARALLEL TEST CODE #############################
# Now loop over all sub-sets - - - - - - - - - - - - - - - - - - - - - - - -
# (pre-process them first before giving them to the actual linear assignment
# method)
#
lap_lap_start_time = time.time()
lap_comm_time = 0.0
sub_set_cnt = 0 # A round robin counter, used for parallelism
sub_set_rows = sub_sets.keys()
sub_set_rows.sort() # Needed to make the same on all processes
for seed_row in sub_set_rows:
# Distribute sub-sets equally to all processors
#
if ((sub_set_cnt % parallel.size()) == parallel.rank()):
row_list = sub_sets[seed_row]
row_list.sort()
print '1:'
print '1: Sub-set %i of %i with seed row %i contains %i rows' % \
(sub_set_cnt, num_sub_sets, seed_row, len(row_list))
print '3: Sub-set rows: %s' % (str(row_list))
if (len(row_list) == 1): # Special case: One row only - - - - - - - - -
max_weight = -99999.9
max_col = -1
row_dict = work_dict[row_list[0]] # Get the dictionary for this row
# Find element with largest weight
#
for col_num in row_dict:
weight = row_dict[col_num]
if (weight > max_weight):
max_weight = weight
max_col = col_num
# Assignment dictionary is of form col_num:row_num
#
tmp_assign_dict = {max_col:row_list[0]} # Make record pair dictionary
print '2: Special case sub-set with one row only, ' + \
'assignment pair: (%i,%i)' % (row_list[0], max_col)
else: # General case with more than one row - - - - - - - - - - - - - -
# Get minimal and maximal weights, and lists with row and column
# numbers
#
min_weight = 999999.9
max_weight = -999999.9
col_numbers = {}
row_col_numbers = {}
for row_num in row_list: # Loop over rows in this sub-set
row_dict = work_dict[row_num] # Get the dictionary for this row
row_col_numbers[row_num] = 1
for col_num in row_dict:
weight = row_dict[col_num]
col_numbers[col_num] = 1
row_col_numbers[col_num] = 1
if (weight < min_weight):
min_weight = weight
if (weight > max_weight):
max_weight = weight
print '3: Minimal and maximal weight: %.3f / %.3f' % \
(min_weight, max_weight)
row_numbers = work_dict.keys()
col_numbers = col_numbers.keys()
row_numbers.sort()
col_numbers.sort()
num_rows = len(row_numbers)
num_cols = len(col_numbers)
row_col_numbers = row_col_numbers.keys()
row_col_numbers.sort()
#print '1: Row numbers: %s' % (str(row_numbers))
#print '1: Column numbers: %s' % (str(col_numbers))
#print '1: Row/colum numbers: %s' % (str(row_col_numbers))
#print '1: Number of unique weights: %i' % (len(weight_dict))
# Deal with the special case that there is only one column number - - -
#
if (num_cols == 1):
max_weight = -99999.9
max_row = -1
col_num = col_numbers[0] # Get the column number
# Find element with largest weight
#
for row_num in row_list: # Loop over rows
# Get only weight in row
#
row_weight = work_dict[row_num].values()[0]
if (row_weight > max_weight):
max_weight = row_weight
max_row = row_num
# Assignment dictionary is of form col_num:row_num
#
tmp_assign_dict = {col_num:max_row} # Make record pair dictionary
print '2: Special case sub-set with one column only, ' + \
'assignment pair: (%i,%i)' % (max_row, col_num)
else: # General case with more than one row and column - - - - - - - -
# Construct the cost dictionary - - - - - - - - - - - - - - - - - - -
#
cost_dict = {}
dim = len(row_col_numbers) # Final dimension of the LAP
min_cost = -max_weight * (dim + 1) # Use original wieghts
for row_num in row_list: # Loop over rows
row_dict = work_dict[row_num]
# Get the column numbers in this row
#
col_list = row_dict.keys()
col_list.sort()
row_cost_dict = cost_dict.get(row_num, {})
for col_num in col_list:
weight = row_dict[col_num]
cost = weight * (dim + 1) # Use original weights
row_cost_dict[col_num] = cost # And store into row dictionary
# Insert symmetric element as well (if not on diagonal)
#
if (row_num != col_num):
row_cost_dict2 = cost_dict.get(col_num,{})
if (row_num not in row_cost_dict2): # Only insert if not there
if (process_type == 'deduplication'):
row_cost_dict2[row_num] = cost # Insert symmetric cost
else: # Linkage process
row_cost_dict2[row_num] = min_cost # Insert minimal cost
# And insert diagonal element if there is none
#
if (not row_cost_dict2.has_key(col_num)):
row_cost_dict2[col_num] = min_cost
cost_dict[col_num] = row_cost_dict2
# Make sure there is a diagonal element (for feasibility)
#
if (not row_cost_dict.has_key(row_num)):
row_cost_dict[row_num] = min_cost
# If more than MAX_ROW_ELEMENTS elements in row only take the
# largest (following an idea by William Winkler)
#
if (len(row_cost_dict) > MAX_ROW_ELEMENTS):
row_col_numbers = row_cost_dict.keys()
row_weights = row_cost_dict.values()
row_elem_list = map(None, row_weights, row_col_numbers)
row_elem_list.sort()
diag_weight = row_cost_dict[row_num] # Keep diagonal element
row_cost_dict = {row_num:diag_weight}
##print ' '
##print '****** row_elem_list: %s' % (str(row_elem_list))
##print ' '
for (weight, col_num) in row_elem_list[-MAX_ROW_ELEMENTS:]:
row_cost_dict[col_num] = weight
# Insert row into cost dictionary
#
cost_dict[row_num] = row_cost_dict
# Get the final row and column numbers - - - - - - - - - - - - - - -
#
row_numbers = cost_dict.keys()
col_numbers = {}
for row_dict in cost_dict.values():
col_numbers.update(row_dict)
col_numbers = col_numbers.keys()
row_numbers.sort()
col_numbers.sort()
# Check if number of rows and columns are equal - - - - - - - - - - -
#
if (len(row_numbers) != len(col_numbers)):
print 'error:Different number of rows (%i) and columns (%i)' \
% (len(row_numbers), len(col_numbers))
raise Exception
print '1: Cost dictionary with %i rows/columns given to ' % \
(len(row_numbers)) + 'assignment method %s:' % (lap_method)
print '2: Row numbers: %s' % (str(row_numbers))
print '2: Column numbers: %s' % (str(row_numbers))
print '2: Minimal weight: %3f' % (min_weight)
print '2: Maximal weight: %3f' % (max_weight)
print '3: Cost dictionary: %s' % (str(cost_dict))
print '3: Process type: %s' % (process_type)
#################### START PARALLEL TEST CODE #######################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = cost_dict.keys()
tmp_list.sort()
tmp_str = str(sub_set_cnt)+':: '+ str(min_weight) + ' / ' + \
str(max_weight) + ', ' + str(row_numbers) + ', ' + \
process_type + '::'
for k in tmp_list:
tmp_list2 = cost_dict[k].items()
tmp_list2.sort()
tmp_str = tmp_str + ' ' + str(tmp_list2) + ' / '
f = open('lap-calling-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'a')
f.write(tmp_str+os.linesep)
f.close()
#################### END PARALLEL TEST CODE #########################
# Call the lap method which returns an assignment dictionary - - - -
#
if (lap_method == 'auction'):
tmp_assign_dict = auction(cost_dict, min_weight, max_weight, \
row_numbers, col_numbers)
else:
print 'error:LAP method %s not implemented' % (lap_method)
raise Exception
# If run in parallel, send temporary assignment dictionary process 0 - -
#
if (parallel.rank() > 0):
tmp_time = time.time()
parallel.send(tmp_assign_dict, 0)
lap_comm_time += (time.time() - tmp_time)
print '1: Sent assignment dictionary with %i entries to process' \
% (len(tmp_assign_dict)) + ' 0'
# Only process 0 inserts temporary assignment dictionary into results - - -
#
if (parallel.rank() == 0):
# Receive assignment dictionary from other process if necessary
#
p = (sub_set_cnt % parallel.size()) # Process number to receive from
if (p != 0):
tmp_time = time.time()
tmp_assign_dict = parallel.receive(p)
lap_comm_time += (time.time() - tmp_time)
print '1: Received subset %i of %i assignment dictionary with ' % \
(sub_set_cnt, num_sub_sets) + '%i entries from process %i' % \
(len(tmp_assign_dict), p)
# Post-process the assignment dictionary - - - - - - - - - - - - - - - -
#
assign_pairs = {}
for rec_num_b in tmp_assign_dict:
rec_num_a = tmp_assign_dict[rec_num_b]
# Now check if this record pair is in the original results dictionary
#
if (rec_num_a in results_dict):
row_dict = results_dict[rec_num_a]
if (rec_num_b in row_dict):
weight = row_dict[rec_num_b]
# Insert into dictionary of potential record pairs
#
assign_pairs[(rec_num_a, rec_num_b)] = weight
#################### START PARALLEL TEST CODE ###########################
if (SAVE_PARALLEL_TEST_FILES == True):
tmp_list = tmp_assign_dict.items()
tmp_list.sort()
tmp_list2 = assign_pairs.items()
tmp_list2.sort()
tmp_list3 = sub_sets[seed_row]
tmp_list3.sort()
f = open('assignments-'+str(parallel.rank())+'-'+ \
str(parallel.size()),'a')
f.write(str(sub_set_cnt)+', '+str(seed_row)+os.linesep)
f.write(str(tmp_list)+os.linesep)
f.write(str(tmp_list2)+os.linesep)
f.write(str(tmp_list3)+os.linesep)
f.write(os.linesep)
f.close()
#################### END PARALLEL TEST CODE #############################
# Sort the assigned pairs according to their weight
#
assign_weights = assign_pairs.values() # Get the weights in a list
assign_rec_pairs = assign_pairs.keys() # And the record pairs
assign_pair_list = map(None, assign_weights, assign_rec_pairs)
assign_pair_list.sort()
num_assigned_pairs = 0 # Number of assigned pairs for this sub-set
dedup_check_rec_nums = {} # Already assigned record numbers
while (assign_pair_list != []): # Now check all record pairs
check_pair = assign_pair_list.pop() # Get largest weight record pair
weight = check_pair[0]
rec_num_a = check_pair[1][0]
rec_num_b = check_pair[1][1]
rec_pair = (rec_num_a, rec_num_b)
# Now check if a record pair has already been used in an assignment
# and for a deduplication process also check if any of the two
# records has been used in an assignment
#
if ((process_type == 'linkage') and \
(rec_num_a not in used_rec_nums_a) and \
(rec_num_b not in used_rec_nums_b)) or \
((process_type == 'deduplication') and \
(rec_num_a not in used_rec_nums) and \
(rec_num_b not in used_rec_nums)):
# For deduplication insert record numbers into used record numbers
#
if (process_type == 'deduplication'):
used_rec_nums[rec_num_a] = True
used_rec_nums[rec_num_b] = True
else:
used_rec_nums_a[rec_num_a] = True
used_rec_nums_b[rec_num_b] = True
if (rec_pair not in lap_results):
lap_results[rec_pair] = True
num_assigned_pairs += 1
else:
print 'warning:Record pair (%i,%i) already in LAP results' \
% (rec_num_a, rec_num_b)
print '2: Inserted %i (out of %i) record pairs into LAP ' % \
(num_assigned_pairs, len(tmp_assign_dict)) + 'results'
sub_set_cnt += 1
# Report progress every 10% (only if more than 100 sub-sets) - - - - - - -
#
if (num_sub_sets >= 100) and (sub_set_cnt % int(num_sub_sets / 10) == 0):
used_time = time.time() - lap_lap_start_time
perc_done = 100.0 * sub_set_cnt / num_sub_sets
sub_set_time = used_time / sub_set_cnt
todo_time = (num_sub_sets - sub_set_cnt) * sub_set_time
used_time_string = output.time_string(used_time)
todo_time_string = output.time_string(todo_time)
sub_set_time_string = output.time_string(sub_set_time)
print '1: Processed %.1f%% (%i/%i) of sub-sets in %s' % \
(perc_done, sub_set_cnt, num_sub_sets, used_time_string) + \
' (%s per sub-set)' % (sub_set_time_string)
print '1: Estimated %s until finished' % (todo_time_string)
print '1: Total number of assignments: %i' % (len(lap_results))
print '1: Number of rows in original results dictionary: %i' % \
(len(results_dict))
#################### START TEST CODE ########################################
# Test if a record only appears once in the lap results dictionary
#
if (DO_TESTS == True) and (parallel.rank() == 0):
if (process_type == 'deduplication'):
test_dict = {}
for (rec_a, rec_b) in lap_results:
if (test_dict.has_key(rec_a)):
print 'warning:Record %i is already in the test dictionary' % \
(rec_a)+' rec_pair: (%i,%i)' % (rec_a, rec_b)
else:
test_dict[rec_a] = True
if (test_dict.has_key(rec_b)):
print 'warning:Record %i is already in the test dictionary' % \
(rec_b)+' rec_pair: (%i,%i)' % (rec_a, rec_b)
else:
test_dict[rec_b] = 1
else: # Linkage process
test_dict_a = {}
test_dict_b = {}
for (rec_a, rec_b) in lap_results:
if (test_dict_a.has_key(rec_a)):
print 'warning:Record %s is already in test dictionary A' % \
(str(rec_a))
else:
test_dict_a[rec_a] = 1
if (test_dict_b.has_key(rec_b)):
print 'warning:Record %s is already in test dictionary B' % \
(str(rec_b))
else:
test_dict_b[rec_b] = 1
#################### END TEST CODE ##########################################
lap_stop_time = time.time()
lap_lap_time = lap_stop_time - lap_lap_start_time
lap_total_time = lap_stop_time - lap_start_time
lap_pair_extract_time_string = output.time_string(lap_pair_extract_time)
lap_subset_total_time_string = output.time_string(lap_subset_total_time)
lap_lap_time_string = output.time_string(lap_lap_time)
if (parallel.size() > 1):
lap_comm_time_string = output.time_string(lap_comm_time)
lap_total_time_string = output.time_string(lap_total_time)
print '1:'
print '1: Finished linear record pair assignment procedure'
print '1: Time for extracting unique record pairs: %s' % \
(lap_pair_extract_time_string)
print '1: Time for creating record sub-sets: %s' % \
(lap_subset_total_time_string)
print '1: Time for linear assignment algorithm: %s' % \
(lap_lap_time_string)
if (parallel.size() > 1):
print '1: Time for communication: %s' % \
(lap_comm_time_string)
print '1: Total time for linear assignment: %s' % \
(lap_total_time_string)
print '1:'
return lap_results