def run(self, args):
#read inputs
from prime.postrefine.mod_input import process_input, read_pickles
iparams, txt_out_input = process_input(args)
print txt_out_input
f = open(iparams.run_no+'/log.txt', 'w')
f.write(txt_out_input)
f.close()
#if solution pickle is given, return the file name
if iparams.indexing_ambiguity.index_basis_in is not None:
if iparams.indexing_ambiguity.index_basis_in.endswith('.pickle'):
return iparams.indexing_ambiguity.index_basis_in, iparams
#read all integration pickles
frame_files = read_pickles(iparams.data)
n_frames = len(frame_files)
if n_frames == 0:
print "No integration pickle found. Exit program."
return None, iparams
#exit if no problem
if self.should_terminate(iparams, frame_files[0]):
print "No indexing ambiguity problem. Set index_ambiguity.mode = Forced and assigned_basis = list of basis formats to solve pseudo-twinning problem."
return None, iparams
#continue with (Auto - alt>1, find solution), (Auto - alt>1, mtz)
#(Forced - assigned_basis, mtz), (Forced - assigned_basis, find solution)
#*************************************************
#if mtz file is given, use it to solve the problem
sol_fname = iparams.run_no+'/index_ambiguity/solution_pickle.pickle'
if iparams.indexing_ambiguity.index_basis_in is not None:
if iparams.indexing_ambiguity.index_basis_in.endswith('.mtz'):
mxh = mx_handler()
flag_ref_found, miller_array_ref = mxh.get_miller_array_from_reflection_file(iparams.indexing_ambiguity.index_basis_in)
if flag_ref_found == False:
print "Reference mtz file not found. Set indexing_ambiguity.index_basis_in = None to enable auto generate the solutions."
return None, iparams
else:
frames = [(i, frame_files[i], iparams, miller_array_ref) for i in range(n_frames)]
cc_results = pool_map(
iterable=frames,
func=solve_with_mtz_mproc,
processes=iparams.n_processors)
sol_pickle = {}
for result in cc_results:
pickle_filename, index_basis = result
sol_pickle[pickle_filename] = index_basis
pickle.dump(sol_pickle, open(sol_fname,"wb"))
return sol_fname, iparams
#*************************************************
#solve with Brehm & Diederichs - sample size n_sample_frames then bootstrap the rest
frames = [(i, frame_files[i], iparams) for i in random.sample(range(n_frames), iparams.indexing_ambiguity.n_sample_frames)]
#get observations list
print "Reading observations"
alt_dict_results = pool_map(
iterable=frames,
func=get_obs_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
obs_list = []
for result in alt_dict_results:
alt_dict, pickle_filename = result
if alt_dict is not None:
for key in alt_dict.keys():
frame_dup_files.append(pickle_filename)
frame_keys.append(key)
obs_list.append(alt_dict[key])
frames = [(i, frame_dup_files[i], frame_keys[i], obs_list[i], obs_list) for i in range(len(frame_dup_files))]
#calculate r
print "Calculating R"
calc_r_results = pool_map(
iterable=frames,
func=calculate_r_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
r_matrix = []
for result in calc_r_results:
if result is not None:
pickle_filename, index_basis, r_set = result
frame_dup_files.append(pickle_filename)
frame_keys.append(index_basis)
if len(r_matrix) == 0:
r_matrix = r_set
else:
r_matrix = np.append(r_matrix, r_set, axis=0)
#choose groups with best CC
print "Selecting frames with best R"
i_mean_r = np.argsort(np.mean(r_matrix, axis=1))[::-1]
r_matrix_sorted = r_matrix[i_mean_r]
frame_dup_files_sorted = np.array(frame_dup_files)[i_mean_r]
frame_keys_sorted = np.array(frame_keys)[i_mean_r]
frame_dup_files_sel = []
for frame_file, frame_key, r_set in zip(frame_dup_files_sorted, frame_keys_sorted, r_matrix_sorted):
if frame_file not in frame_dup_files_sel:
frame_dup_files_sel.append(frame_file)
print frame_file, frame_key, np.mean(r_set)
if len(frame_dup_files_sel) >= iparams.indexing_ambiguity.n_selected_frames:
print 'Found all %6.0f good frames'%(len(frame_dup_files_sel))
break
##
#rebuild observations and r_matrix
frames = [(i, frame_dup_files_sel[i], iparams) for i in range(len(frame_dup_files_sel))]
#get observations list
print "Re-reading observations"
alt_dict_results = pool_map(
iterable=frames,
func=get_obs_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
obs_list = []
for result in alt_dict_results:
alt_dict, pickle_filename = result
if alt_dict is not None:
for key in alt_dict.keys():
frame_dup_files.append(pickle_filename)
frame_keys.append(key)
obs_list.append(alt_dict[key])
frames = [(i, frame_dup_files[i], frame_keys[i], obs_list[i], obs_list) for i in range(len(frame_dup_files))]
#calculate r
print "Re-calculating R"
calc_r_results = pool_map(
iterable=frames,
func=calculate_r_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
r_matrix = []
for result in calc_r_results:
if result is not None:
pickle_filename, index_basis, r_set = result
frame_dup_files.append(pickle_filename)
frame_keys.append(index_basis)
if len(r_matrix) == 0:
r_matrix = r_set
else:
r_matrix = np.append(r_matrix, r_set, axis=0)
print "Minimizing frame distance"
idah = indamb_handler()
x_set = idah.optimize(r_matrix, flag_plot=iparams.flag_plot)
x_pickle = {'frame_dup_files':frame_dup_files, 'frame_keys':frame_keys, \
'r_matrix':r_matrix, 'x_set':x_set}
pickle.dump(x_pickle, open(iparams.run_no+'/index_ambiguity/x.out',"wb"))
print "Clustering results"
kmh = kmeans_handler()
k = 2**(len(idah.get_observations(frame_dup_files[0], iparams))-1)
centroids, labels = kmh.run(x_set, k, flag_plot=iparams.flag_plot)
print "Get solution pickle"
sample_fname = iparams.run_no+'/index_ambiguity/sample.lst'
sol_pickle = idah.assign_basis(frame_dup_files, frame_keys, labels, k, sample_fname)
pickle.dump(sol_pickle, open(sol_fname,"wb"))
#if more frames found, merge the sample frames to get a reference set
#that can be used for breaking the ambiguity.
if n_frames > iparams.indexing_ambiguity.n_selected_frames:
print "Breaking the indexing ambiguity for the remaining images."
old_iparams_data = iparams.data[:]
iparams.data = [sample_fname]
iparams.indexing_ambiguity.index_basis_in = sol_fname
grh = genref_handler()
grh.run_by_params(iparams)
mh = merge_handler()
mh.run_by_params(iparams)
DIR = iparams.run_no+'/mtz/'
file_no_list = [int(fname.split('.')[0]) for fname in os.listdir(DIR)]
if len(file_no_list) > 0:
hklref_indamb = DIR + str(max(file_no_list)) + '.mtz'
print "Bootstrap reference reflection set:", hklref_indamb
#setup a list of remaining frames
frame_files_remain = []
for frame in frame_files:
if frame not in sol_pickle:
frame_files_remain.append(frame)
#determine index basis
mxh = mx_handler()
flag_ref_found, miller_array_ref = mxh.get_miller_array_from_reflection_file(hklref_indamb)
frames = [(i, frame_files_remain[i], iparams, miller_array_ref) for i in range(len(frame_files_remain))]
cc_results = pool_map(
iterable=frames,
func=solve_with_mtz_mproc,
processes=iparams.n_processors)
for result in cc_results:
pickle_filename, index_basis = result
sol_pickle[pickle_filename] = index_basis
iparams.data = old_iparams_data[:]
#write out solution pickle
pickle.dump(sol_pickle, open(sol_fname,"wb"))
#write out text output
txt_out = "Solving indexing ambiguity complete. Solution file saved to "+sol_fname+"\n"
f = open(iparams.run_no+'/log.txt', 'a')
f.write(txt_out)
f.close()
return sol_fname, iparams
def run(self, args):
#read inputs
from prime.postrefine.mod_input import process_input, read_pickles
iparams, txt_out_input = process_input(args)
print txt_out_input
f = open(iparams.run_no+'/log.txt', 'w')
f.write(txt_out_input)
f.close()
#if solution pickle is given, return the file name
if iparams.indexing_ambiguity.index_basis_in is not None:
if iparams.indexing_ambiguity.index_basis_in.endswith('.pickle'):
return iparams.indexing_ambiguity.index_basis_in, iparams
#read all integration pickles
frame_files = read_pickles(iparams.data)
n_frames = len(frame_files)
if n_frames == 0:
print "No integration pickle found. Exit program."
return None, iparams
#exit if no problem
if self.should_terminate(iparams, frame_files[0]):
print "No indexing ambiguity problem. Set index_ambiguity.mode = Forced and assigned_basis = list of basis formats to solve pseudo-twinning problem."
return None, iparams
#continue with (Auto - alt>1, find solution), (Auto - alt>1, mtz)
#(Forced - assigned_basis, mtz), (Forced - assigned_basis, find solution)
#*************************************************
#if mtz file is given, use it to solve the problem
sol_fname = iparams.run_no+'/index_ambiguity/solution_pickle.pickle'
if iparams.indexing_ambiguity.index_basis_in is not None:
if iparams.indexing_ambiguity.index_basis_in.endswith('.mtz'):
mxh = mx_handler()
flag_ref_found, miller_array_ref = mxh.get_miller_array_from_reflection_file(iparams.indexing_ambiguity.index_basis_in)
if flag_ref_found == False:
print "Reference mtz file not found. Set indexing_ambiguity.index_basis_in = None to enable auto generate the solutions."
return None, iparams
else:
frames = [(i, frame_files[i], iparams, miller_array_ref) for i in range(n_frames)]
cc_results = pool_map(
iterable=frames,
func=solve_with_mtz_mproc,
processes=iparams.n_processors)
sol_pickle = {}
for result in cc_results:
pickle_filename, index_basis = result
sol_pickle[pickle_filename] = index_basis
pickle.dump(sol_pickle, open(sol_fname,"wb"))
return sol_fname, iparams
#*************************************************
#solve with Brehm & Diederichs - sample size n_sample_frames then bootstrap the rest
frames = [(i, frame_files[i], iparams) for i in random.sample(range(n_frames), iparams.indexing_ambiguity.n_sample_frames)]
#get observations list
print "Reading observations"
alt_dict_results = pool_map(
iterable=frames,
func=get_obs_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
obs_list = []
for result in alt_dict_results:
alt_dict, pickle_filename = result
if alt_dict is not None:
for key in alt_dict.keys():
frame_dup_files.append(pickle_filename)
frame_keys.append(key)
obs_list.append(alt_dict[key])
frames = [(i, frame_dup_files[i], frame_keys[i], obs_list[i], obs_list) for i in range(len(frame_dup_files))]
#calculate r
print "Calculating R"
calc_r_results = pool_map(
iterable=frames,
func=calculate_r_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
r_matrix = []
for result in calc_r_results:
if result is not None:
pickle_filename, index_basis, r_set = result
frame_dup_files.append(pickle_filename)
frame_keys.append(index_basis)
if len(r_matrix) == 0:
r_matrix = r_set
else:
r_matrix = np.append(r_matrix, r_set, axis=0)
#choose groups with best CC
print "Selecting frames with best R"
i_mean_r = np.argsort(np.mean(r_matrix, axis=1))[::-1]
r_matrix_sorted = r_matrix[i_mean_r]
frame_dup_files_sorted = np.array(frame_dup_files)[i_mean_r]
frame_keys_sorted = np.array(frame_keys)[i_mean_r]
frame_dup_files_sel = []
for frame_file, frame_key, r_set in zip(frame_dup_files_sorted, frame_keys_sorted, r_matrix_sorted):
if frame_file not in frame_dup_files_sel:
frame_dup_files_sel.append(frame_file)
print frame_file, frame_key, np.mean(r_set)
if len(frame_dup_files_sel) >= iparams.indexing_ambiguity.n_selected_frames:
print 'Found all %6.0f good frames'%(len(frame_dup_files_sel))
break
##
#rebuild observations and r_matrix
frames = [(i, frame_dup_files_sel[i], iparams) for i in range(len(frame_dup_files_sel))]
#get observations list
print "Re-reading observations"
alt_dict_results = pool_map(
iterable=frames,
func=get_obs_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
obs_list = []
for result in alt_dict_results:
alt_dict, pickle_filename = result
if alt_dict is not None:
for key in alt_dict.keys():
frame_dup_files.append(pickle_filename)
frame_keys.append(key)
obs_list.append(alt_dict[key])
frames = [(i, frame_dup_files[i], frame_keys[i], obs_list[i], obs_list) for i in range(len(frame_dup_files))]
#calculate r
print "Re-calculating R"
calc_r_results = pool_map(
iterable=frames,
func=calculate_r_mproc,
processes=iparams.n_processors)
frame_dup_files = []
frame_keys = []
r_matrix = []
for result in calc_r_results:
if result is not None:
pickle_filename, index_basis, r_set = result
frame_dup_files.append(pickle_filename)
frame_keys.append(index_basis)
if len(r_matrix) == 0:
r_matrix = r_set
else:
r_matrix = np.append(r_matrix, r_set, axis=0)
print "Minimizing frame distance"
idah = indamb_handler()
x_set = idah.optimize(r_matrix, flag_plot=iparams.flag_plot)
x_pickle = {'frame_dup_files':frame_dup_files, 'frame_keys':frame_keys, \
'r_matrix':r_matrix, 'x_set':x_set}
pickle.dump(x_pickle, open(iparams.run_no+'/index_ambiguity/x.out',"wb"))
print "Clustering results"
kmh = kmeans_handler()
k = 2**(len(idah.get_observations(frame_dup_files[0], iparams))-1)
centroids, labels = kmh.run(x_set, k, flag_plot=iparams.flag_plot)
print "Get solution pickle"
sample_fname = iparams.run_no+'/index_ambiguity/sample.lst'
sol_pickle = idah.assign_basis(frame_dup_files, frame_keys, labels, k, sample_fname)
pickle.dump(sol_pickle, open(sol_fname,"wb"))
#if more frames found, merge the sample frames to get a reference set
#that can be used for breaking the ambiguity.
if n_frames > iparams.indexing_ambiguity.n_selected_frames:
print "Breaking the indexing ambiguity for the remaining images."
old_iparams_data = iparams.data[:]
iparams.data = [sample_fname]
iparams.indexing_ambiguity.index_basis_in = sol_fname
grh = genref_handler()
grh.run_by_params(iparams)
mh = merge_handler()
mh.run_by_params(iparams)
DIR = iparams.run_no+'/mtz/'
file_no_list = [int(fname.split('.')[0]) for fname in os.listdir(DIR)]
if len(file_no_list) > 0:
hklref_indamb = DIR + str(max(file_no_list)) + '.mtz'
print "Bootstrap reference reflection set:", hklref_indamb
#setup a list of remaining frames
frame_files_remain = []
for frame in frame_files:
if frame not in sol_pickle:
frame_files_remain.append(frame)
#determine index basis
mxh = mx_handler()
flag_ref_found, miller_array_ref = mxh.get_miller_array_from_reflection_file(hklref_indamb)
frames = [(i, frame_files_remain[i], iparams, miller_array_ref) for i in range(len(frame_files_remain))]
cc_results = pool_map(
iterable=frames,
func=solve_with_mtz_mproc,
processes=iparams.n_processors)
for result in cc_results:
pickle_filename, index_basis = result
sol_pickle[pickle_filename] = index_basis
iparams.data = old_iparams_data[:]
#write out solution pickle
pickle.dump(sol_pickle, open(sol_fname,"wb"))
#write out text output
txt_out = "Solving indexing ambiguity complete. Solution file saved to "+sol_fname+"\n"
f = open(iparams.run_no+'/log.txt', 'a')
f.write(txt_out)
f.close()
return sol_fname, iparams
def run(self, args):
#read inputs
from prime.postrefine.mod_input import process_input, read_pickles
iparams, txt_out_input = process_input(args)
print txt_out_input
with open(os.path.join(iparams.run_no, self.module_name, 'log.txt'),
'w') as f:
f.write(txt_out_input)
#read all integration pickles
frame_files = read_pickles(iparams.data)
n_frames = len(frame_files)
if n_frames == 0:
print "No integration pickle found. Exit program."
return None, iparams
#start
if iparams.isoform_cluster.isorefin:
#get collection of iso. ref. reflection set.
mxh = mx_handler()
miller_array_ref_set = []
for isorefin in iparams.isoform_cluster.isorefin:
flag_ref_found, miller_array_ref = mxh.get_miller_array_from_reflection_file(
isorefin)
if flag_ref_found:
miller_array_ref_set.append(miller_array_ref)
#get observation list
frame_files_sel, obs_list = self.get_observation_set(
iparams, frame_files, n_frames)
if miller_array_ref_set:
frames = [(i, frame_files_sel[i], obs_list[i], iparams,
miller_array_ref_set) for i in range(len(obs_list))]
cc_results = pool_map(iterable=frames,
func=solve_with_mtz_mproc,
processes=iparams.n_processors)
sol_pickle = {}
for result in cc_results:
pickle_filename, cluster_id = result
sol_pickle[pickle_filename] = cluster_id
write_out_solutions(iparams, sol_pickle)
txt_out = "Cluster images with given " + str(
len(miller_array_ref_set)
) + " mtz files completed. Use cluster_0.lst - cluster_k.lst (for k clusters) for merging.\n"
print txt_out
with open(
os.path.join(iparams.run_no, self.module_name,
'log.txt'), 'a') as f:
f.write(txt_out)
return
#*************************************************
#solve with Brehm & Diederichs - sample size n_sample_frames then bootstrap the rest
txt_out = "Cluster images with B&D algorithms.\n"
frame_files_sel, obs_list = self.get_observation_set(
iparams, frame_files, iparams.isoform_cluster.n_sample_frames)
frames = [(i, frame_files_sel[i], obs_list[i], obs_list)
for i in range(len(frame_files_sel))]
#calculate r
print "Calculating R"
calc_r_results = pool_map(iterable=frames,
func=calculate_r_mproc,
processes=iparams.n_processors)
frame_files_sel = []
r_matrix = []
obs_list = []
for result in calc_r_results:
if result:
pickle_filename, r_set, obs = result
frame_files_sel.append(pickle_filename)
obs_list.append(obs)
if len(r_matrix) == 0:
r_matrix = r_set
else:
r_matrix = np.append(r_matrix, r_set, axis=0)
#choose groups with best R
print "Selecting frames with best R"
i_mean_r = np.argsort(np.mean(r_matrix, axis=1))[::-1]
r_matrix_sorted = r_matrix[i_mean_r]
frame_files_sorted = np.array(frame_files_sel)[i_mean_r]
obs_list_sorted = np.array(obs_list)[i_mean_r]
frame_files_sel = []
obs_sel = []
for frame_file, r_set, obs in zip(frame_files_sorted, r_matrix_sorted,
obs_list_sorted):
if frame_file not in frame_files_sel:
frame_files_sel.append(frame_file)
obs_sel.append(obs)
print frame_file, np.mean(r_set)
if len(frame_files_sel
) >= iparams.isoform_cluster.n_selected_frames:
print 'Found all %6.0f good frames' % (
len(frame_files_sel))
break
#Recalculate r for the new selected list
frames = [(i, frame_files_sel[i], obs_sel[i], obs_sel)
for i in range(len(frame_files_sel))]
print "Re-calculating R"
calc_r_results = pool_map(iterable=frames,
func=calculate_r_mproc,
processes=iparams.n_processors)
frame_files_sel = []
r_matrix = []
obs_list = []
for result in calc_r_results:
if result:
pickle_filename, r_set, obs = result
frame_files_sel.append(pickle_filename)
obs_list.append(obs)
if len(r_matrix) == 0:
r_matrix = r_set
else:
r_matrix = np.append(r_matrix, r_set, axis=0)
print "Minimizing frame distance"
isoch = isoform_cluster_handler()
x_set = isoch.optimize(r_matrix, flag_plot=iparams.flag_plot)
print "Clustering results"
kmh = kmeans_handler()
k = iparams.isoform_cluster.n_clusters
centroids, labels = kmh.run(x_set, k, flag_plot=iparams.flag_plot)
print "Get solution pickle and cluster files list"
sol_pickle, cluster_files = isoch.assign_cluster(frame_files_sel, labels, k, \
os.path.join(iparams.run_no,self.module_name))
#if more frames found, merge the sample frames to get a reference set
#that can be used for breaking the ambiguity.
if n_frames > iparams.isoform_cluster.n_selected_frames:
print "Assign cluster_id for the remaining images."
old_iparams_data = iparams.data[:]
miller_array_ref_set = []
from prime.command_line.postrefine import scale_frames, merge_frames
for i in range(k):
#generate a reference set from solved frames
with open(cluster_files[i]) as f:
frame_files_processed = f.read().split('\n')[:-1]
scaled_pres_set = scale_frames(
range(len(frame_files_processed)), frame_files_processed,
iparams)
mdh, txt_merge_out = merge_frames(scaled_pres_set, iparams, \
mtz_out_prefix=os.path.join(self.module_name,'cluster_'+str(i)))
miller_array_ref_set.append(mdh.miller_array_merge)
txt_out += txt_merge_out
#setup a list of remaining frames
frame_files_remain = [
frame for frame in frame_files if frame not in sol_pickle
]
frame_files_remain_sel, obs_remain_sel_list = self.get_observation_set(iparams, \
frame_files_remain, len(frame_files_remain))
frames = [(i, frame_files_remain_sel[i], obs_remain_sel_list[i],
iparams, miller_array_ref_set)
for i in range(len(obs_remain_sel_list))]
cc_results = pool_map(iterable=frames,
func=solve_with_mtz_mproc,
processes=iparams.n_processors)
for result in cc_results:
if result:
pickle_filename, cluster_id = result
sol_pickle[pickle_filename] = cluster_id
iparams.data = old_iparams_data[:]
#write out solution pickle
write_out_solutions(iparams, sol_pickle)
#write out text output
txt = "Cluster images completed. Use cluster_0.lst - cluster_k.lst (for k clusters) for merging.\n"
txt_out += txt
print txt
with open(os.path.join(iparams.run_no, self.module_name, 'log.txt'),
'a') as f:
f.write(txt_out)