def simplify_lines_AllFrame(Input_MoleParentFolder_interval, GroupNum, MoleculeNum, threshold): fileContents = mfc.read_molecule_files_frominf(Input_MoleParentFolder_interval, GroupNum, MoleculeNum) connect_count, frames, cells = mfc.get_frame_count_mole(fileContents) straightness = [] for FrameNum in frames: ## readin molecule backbone information fileContents_setframe = mfc.get_content_setframe(fileContents, FrameNum) CellNumList_setframe = mfc.get_CellNumbers(fileContents_setframe) ## create a list to store turning points of simplify polyline list_knots = [0, len(CellNumList_setframe)-1] ## generate the simplify line simplify_test = simplify_line_test(CellNumList_setframe, threshold) while(simplify_test): ## for first recursion if len(list_knots) == 2: re_time = [0] simplify_line(CellNumList_setframe, 0, len(CellNumList_setframe)-1, list_knots, threshold, re_time) ## downstream recursion else: ## for each segment for i in range(0, len(list_knots) - 2): ## check whether this segment need more recursion if simplify_test_list[i]: re_time = [0] simplify_line(CellNumList_setframe, list_knots[i], list_knots[i+1], list_knots, threshold, re_time) list_knots = sorted(list(set(list_knots))) ## check every segment, decide simplify polyline creation is finished or not simplify_test_list = [] for i in range(0, len(list_knots) - 2): simplify_test_list.append(simplify_line_test(CellNumList_setframe[list_knots[i]:(list_knots[i+1] + 1)], threshold)) simplify_test = max(simplify_test_list) ## get turning positions turning_knots_cellnums = list(np.array(CellNumList_setframe)[list_knots]) ## get information related to turning angles theta_list = angle_list(turning_knots_cellnums) theta_max = max(map(abs, theta_list)) theta_sum = sum(map(abs, theta_list)) theta_net = sum(theta_list) ## estimation test_score_sum = float(1 / math.exp((abs(theta_net) + theta_max) / 2)) ## result report straightness.append([FrameNum, theta_net, theta_max, test_score_sum]) return straightness
def determine_within_forbackbone(BackbonefileContents, SurroundingfileContents, layer, threshold): CellNumList_backbone = mfc.get_CellNumbers(BackbonefileContents) EffectedList = effected_pixels(SurroundingfileContents, layer, threshold) ConditionList = [] for test_cellnum in CellNumList_backbone: condition = determine_within_foronepoint(test_cellnum, EffectedList) ConditionList.append(condition) return ConditionList
def determine_within_forbackbone(BackbonefileContents, SurroundingfileContents,
layer, threshold):
CellNumList_backbone = mfc.get_CellNumbers(BackbonefileContents)
EffectedList = effected_pixels(SurroundingfileContents, layer, threshold)
ConditionList = []
for test_cellnum in CellNumList_backbone:
condition = determine_within_foronepoint(test_cellnum, EffectedList)
ConditionList.append(condition)
return ConditionList
def surrounding_OneMolecule_forframe(display_array, Input_MoleParentFolder, Output_moleParentFolder, Output_plotParentFolder, GroupNum, FrameNum, MoleculeNum = 0, backbone_range = 2, close = False, molecule_filename = " "):
GroupNum = int(GroupNum)
FrameNum = int(FrameNum)
MoleculeNum = int(MoleculeNum)
### data input
grayData_array = fi.get_grayData_frominf(GroupNum, FrameNum)
if molecule_filename == " ":
molecule_filename = "molecule" + MoleculeNum + ".txt"
else:
MoleculeNum = int(re.findall(r"molecule([0-9]*).txt", molecule_filename)[0])
fileContents = mfc.read_molecule_files_fromname(Input_MoleParentFolder, GroupNum, molecule_filename)
inframe = mfc.find_mole_setframe(fileContents, FrameNum)
if(not(inframe)):
print "the molecule is not in this frame! "
exit(1)
molecule_contents_setframe = mfc.get_content_setframe(fileContents, FrameNum)
CellNumList_setframe = mfc.get_CellNumbers(molecule_contents_setframe)
### surrounding intensity acquisition
surrounding_intensity_circle_1 = surrounding_intensity_circle(CellNumList_setframe, grayData_array, display_array, 2, 1, close)
surrounding_intensity_circle_2 = surrounding_intensity_circle(CellNumList_setframe, grayData_array, display_array, 2, 2, close)
surrounding_intensity_circle_3 = surrounding_intensity_circle(CellNumList_setframe, grayData_array, display_array, 2, 3, close)
surrounding_coordinate_1 = surrounding_circle(CellNumList_setframe, 2, 1, close)
surrounding_coordinate_2 = surrounding_circle(CellNumList_setframe, 2, 2, close)
surrounding_coordinate_3 = surrounding_circle(CellNumList_setframe, 2, 3, close)
length = len(surrounding_coordinate_3)
surrounding = np.zeros((length, 6), dtype = int)
surrounding[0:(len(surrounding_intensity_circle_1)),0] = surrounding_intensity_circle_1
surrounding[0:(len(surrounding_intensity_circle_2)),1] = surrounding_intensity_circle_2
surrounding[0:(len(surrounding_intensity_circle_3)),2] = surrounding_intensity_circle_3
surrounding[0:(len(surrounding_coordinate_1)),3] = surrounding_coordinate_1
surrounding[0:(len(surrounding_coordinate_2)),4] = surrounding_coordinate_2
surrounding[0:(len(surrounding_coordinate_3)),5] = surrounding_coordinate_3
### data output
GroupName = "group1-" + str(GroupNum) + "-inca34-outputs/"
FrameName = "frame" + str(FrameNum)
output_groupfolder = os.path.join(Output_moleParentFolder, GroupName)
output_framefolder = os.path.join(output_groupfolder, FrameName)
## for storing data
if(not(os.path.exists(output_framefolder))):
os.makedirs(output_framefolder)
os.chdir(output_framefolder)
molecule_filename_output = "molecule" + str(MoleculeNum) + "_frame" + str(FrameNum)
fileid = open(molecule_filename_output, "w")
fileid.write(" ".join(["intensity1", "intensity2", "intensity3", "coordinate1", "coordinate2", "coordinate3","\n"]))
for line in range(0, length):
line_str = map(str, surrounding[line, :])
line_str.append("\n")
fileid.write(" ".join(line_str))
fileid.close()
print "group", GroupNum, "_frame", FrameNum, "_",molecule_filename, ": surrounding file created!"
## creating folder for successive plotting
output_groupfolder_plot = os.path.join(Output_plotParentFolder, GroupName)
output_framefolder_plot = os.path.join(output_groupfolder_plot, FrameName)
if(not(os.path.exists(output_framefolder_plot))):
os.makedirs(output_framefolder_plot)
return CellNumList_setframe[0] ## return the start cell of this molecule
def surrounding_OneMolecule(Input_MoleParentFolder, Output_moleParentFolder, Output_plotParentFolder, GroupNum, FrameNum, MoleculeNum, select_region = [-1,-1], backbone_range = 2, close = False):
GroupNum = int(GroupNum)
FrameNum = int(FrameNum)
MoleculeNum = int(MoleculeNum)
### data input
grayData_array = fi.get_grayData_frominf(GroupNum, FrameNum)
display_array1 = copy.deepcopy(grayData_array)
display_array2 = copy.deepcopy(grayData_array)
display_array3 = copy.deepcopy(grayData_array)
fileContents = mfc.read_molecule_files_frominf(Input_MoleParentFolder, GroupNum, MoleculeNum)
inframe = mfc.find_mole_setframe(fileContents, FrameNum)
if(not(inframe)):
print "the molecule is not in this frame! "
exit(1)
molecule_contents_setframe = mfc.get_content_setframe(fileContents, FrameNum)
CellNumList_setframe = mfc.get_CellNumbers(molecule_contents_setframe)
heads, tails = mfc.boundary_x(ncol, CellNumList_setframe)
x_min = mfc.get_coordinate(heads[0],ncol)[1]
x_max = mfc.get_coordinate(tails[0],ncol)[1]
if(select_region[0] == -1): select_region[0] = x_min
if(select_region[1] == -1): select_region[1] = x_max
CellNumList_setframe_region = []
for cellnum in CellNumList_setframe:
inregion = mfc.find_cell_inregion_x(cellnum, select_region, ncol)
if(inregion):
CellNumList_setframe_region.append(cellnum)
if(len(CellNumList_setframe) != 0):
### surrounding intensity acquisition
surrounding_intensity_circle_1 = surrounding_intensity_circle(CellNumList_setframe_region, grayData_array, display_array1, 2, 1, close)
surrounding_intensity_circle_2 = surrounding_intensity_circle(CellNumList_setframe_region, grayData_array, display_array2, 2, 2, close)
surrounding_intensity_circle_3 = surrounding_intensity_circle(CellNumList_setframe_region, grayData_array, display_array3, 2, 3, close)
surrounding_coordinate_1 = surrounding_circle(CellNumList_setframe_region, 2, 1, close)
surrounding_coordinate_2 = surrounding_circle(CellNumList_setframe_region, 2, 2, close)
surrounding_coordinate_3 = surrounding_circle(CellNumList_setframe_region, 2, 3, close)
length = len(surrounding_intensity_circle_3)
surrounding = np.zeros((length, 6), dtype = int)
surrounding[0:(len(surrounding_intensity_circle_1)),0] = surrounding_intensity_circle_1
surrounding[0:(len(surrounding_intensity_circle_2)),1] = surrounding_intensity_circle_2
surrounding[0:(len(surrounding_intensity_circle_3)),2] = surrounding_intensity_circle_3
surrounding[0:(len(surrounding_coordinate_1)),3] = surrounding_coordinate_1
surrounding[0:(len(surrounding_coordinate_2)),4] = surrounding_coordinate_2
surrounding[0:(len(surrounding_coordinate_3)),5] = surrounding_coordinate_3
### data output
GroupName = "group1-" + str(GroupNum) + "-inca34-outputs/"
FrameName = "frame" + str(FrameNum)
output_groupfolder = os.path.join(Output_moleParentFolder, GroupName)
## for storing data
if(not(os.path.exists(output_groupfolder))):
os.makedirs(output_groupfolder)
os.chdir(output_groupfolder)
filename = "molecule" + str(MoleculeNum) + "_frame" + str(FrameNum) + ".txt"
fileid = open(filename, "w")
fileid.write(" ".join(["intensity1", "intensity2", "intensity3", "coordinate1", "coordinate2", "coordinate3", "\n"]))
for line in range(0, length):
line_str = map(str, surrounding[line, :])
line_str.append("\n")
fileid.write(" ".join(line_str))
fileid.close()
print "group", GroupNum, "_frame", FrameNum, "_molecule", MoleculeNum, ": surrounding file created!"
## plotting the frame
mole_start_position = mfc.get_coordinate(CellNumList_setframe[0],ncol)
text_position = [mole_start_position[0]-15, mole_start_position[1]]
text = "mole_" + str(MoleculeNum)
plt.figure(FrameNum, figsize=(16, 12), dpi = 100)
mergeplot = plt.imshow(display_array1)
mergeplot.set_cmap(colormap)
plt.text(text_position[1], text_position[0], text, color = "yellow", size = 'medium', weight = 400)
plt.colorbar()
mergeplot.set_clim([np.min(display_array3), image_max])
framename_pdf = "molecule" + str(MoleculeNum) + "_frame" + str(FrameNum) + ".pdf"
framename_png = "molecule" + str(MoleculeNum) + "_frame" + str(FrameNum) + ".png"
plt.savefig(framename_pdf)
plt.savefig(framename_png)
# plt.show()
plt.close()
## save plots to another folder
output_groupfolder_plot = os.path.join(Output_plotParentFolder, GroupName)
if(not(os.path.exists(output_groupfolder_plot))):
os.makedirs(output_groupfolder_plot)
framename_pdf_plot = framename_pdf
framename_png_plot = framename_png
shutil.copyfile(os.path.join(output_groupfolder,framename_pdf),os.path.join(output_groupfolder_plot,framename_pdf_plot))
shutil.copyfile(os.path.join(output_groupfolder,framename_png),os.path.join(output_groupfolder_plot,framename_png_plot))
os.remove(os.path.join(output_groupfolder,framename_pdf))
os.remove(os.path.join(output_groupfolder,framename_png))
else:
print("selected region wrong! no pixel of the molecule in this region..")
def surrounding_OneMolecule_forframe(display_array,
Input_MoleParentFolder,
Output_moleParentFolder,
Output_plotParentFolder,
GroupNum,
FrameNum,
MoleculeNum=0,
backbone_range=2,
close=False,
molecule_filename=" "):
GroupNum = int(GroupNum)
FrameNum = int(FrameNum)
MoleculeNum = int(MoleculeNum)
### data input
grayData_array = fi.get_grayData_frominf(GroupNum, FrameNum)
if molecule_filename == " ":
molecule_filename = "molecule" + MoleculeNum + ".txt"
else:
MoleculeNum = int(
re.findall(r"molecule([0-9]*).txt", molecule_filename)[0])
fileContents = mfc.read_molecule_files_fromname(Input_MoleParentFolder,
GroupNum,
molecule_filename)
inframe = mfc.find_mole_setframe(fileContents, FrameNum)
if (not (inframe)):
print "the molecule is not in this frame! "
exit(1)
molecule_contents_setframe = mfc.get_content_setframe(
fileContents, FrameNum)
CellNumList_setframe = mfc.get_CellNumbers(molecule_contents_setframe)
### surrounding intensity acquisition
surrounding_intensity_circle_1 = surrounding_intensity_circle(
CellNumList_setframe, grayData_array, display_array, 2, 1, close)
surrounding_intensity_circle_2 = surrounding_intensity_circle(
CellNumList_setframe, grayData_array, display_array, 2, 2, close)
surrounding_intensity_circle_3 = surrounding_intensity_circle(
CellNumList_setframe, grayData_array, display_array, 2, 3, close)
surrounding_coordinate_1 = surrounding_circle(CellNumList_setframe, 2, 1,
close)
surrounding_coordinate_2 = surrounding_circle(CellNumList_setframe, 2, 2,
close)
surrounding_coordinate_3 = surrounding_circle(CellNumList_setframe, 2, 3,
close)
length = len(surrounding_coordinate_3)
surrounding = np.zeros((length, 6), dtype=int)
surrounding[0:(len(surrounding_intensity_circle_1)),
0] = surrounding_intensity_circle_1
surrounding[0:(len(surrounding_intensity_circle_2)),
1] = surrounding_intensity_circle_2
surrounding[0:(len(surrounding_intensity_circle_3)),
2] = surrounding_intensity_circle_3
surrounding[0:(len(surrounding_coordinate_1)),
3] = surrounding_coordinate_1
surrounding[0:(len(surrounding_coordinate_2)),
4] = surrounding_coordinate_2
surrounding[0:(len(surrounding_coordinate_3)),
5] = surrounding_coordinate_3
### data output
GroupName = "group1-" + str(GroupNum) + "-inca34-outputs/"
FrameName = "frame" + str(FrameNum)
output_groupfolder = os.path.join(Output_moleParentFolder, GroupName)
output_framefolder = os.path.join(output_groupfolder, FrameName)
## for storing data
if (not (os.path.exists(output_framefolder))):
os.makedirs(output_framefolder)
os.chdir(output_framefolder)
molecule_filename_output = "molecule" + str(MoleculeNum) + "_frame" + str(
FrameNum)
fileid = open(molecule_filename_output, "w")
fileid.write(" ".join([
"intensity1", "intensity2", "intensity3", "coordinate1", "coordinate2",
"coordinate3", "\n"
]))
for line in range(0, length):
line_str = map(str, surrounding[line, :])
line_str.append("\n")
fileid.write(" ".join(line_str))
fileid.close()
print "group", GroupNum, "_frame", FrameNum, "_", molecule_filename, ": surrounding file created!"
## creating folder for successive plotting
output_groupfolder_plot = os.path.join(Output_plotParentFolder, GroupName)
output_framefolder_plot = os.path.join(output_groupfolder_plot, FrameName)
if (not (os.path.exists(output_framefolder_plot))):
os.makedirs(output_framefolder_plot)
return CellNumList_setframe[0] ## return the start cell of this molecule
def surrounding_OneMolecule(Input_MoleParentFolder,
Output_moleParentFolder,
Output_plotParentFolder,
GroupNum,
FrameNum,
MoleculeNum,
select_region=[-1, -1],
backbone_range=2,
close=False):
GroupNum = int(GroupNum)
FrameNum = int(FrameNum)
MoleculeNum = int(MoleculeNum)
### data input
grayData_array = fi.get_grayData_frominf(GroupNum, FrameNum)
display_array1 = copy.deepcopy(grayData_array)
display_array2 = copy.deepcopy(grayData_array)
display_array3 = copy.deepcopy(grayData_array)
fileContents = mfc.read_molecule_files_frominf(Input_MoleParentFolder,
GroupNum, MoleculeNum)
inframe = mfc.find_mole_setframe(fileContents, FrameNum)
if (not (inframe)):
print "the molecule is not in this frame! "
exit(1)
molecule_contents_setframe = mfc.get_content_setframe(
fileContents, FrameNum)
CellNumList_setframe = mfc.get_CellNumbers(molecule_contents_setframe)
heads, tails = mfc.boundary_x(ncol, CellNumList_setframe)
x_min = mfc.get_coordinate(heads[0], ncol)[1]
x_max = mfc.get_coordinate(tails[0], ncol)[1]
if (select_region[0] == -1): select_region[0] = x_min
if (select_region[1] == -1): select_region[1] = x_max
CellNumList_setframe_region = []
for cellnum in CellNumList_setframe:
inregion = mfc.find_cell_inregion_x(cellnum, select_region, ncol)
if (inregion):
CellNumList_setframe_region.append(cellnum)
if (len(CellNumList_setframe) != 0):
### surrounding intensity acquisition
surrounding_intensity_circle_1 = surrounding_intensity_circle(
CellNumList_setframe_region, grayData_array, display_array1, 2, 1,
close)
surrounding_intensity_circle_2 = surrounding_intensity_circle(
CellNumList_setframe_region, grayData_array, display_array2, 2, 2,
close)
surrounding_intensity_circle_3 = surrounding_intensity_circle(
CellNumList_setframe_region, grayData_array, display_array3, 2, 3,
close)
surrounding_coordinate_1 = surrounding_circle(
CellNumList_setframe_region, 2, 1, close)
surrounding_coordinate_2 = surrounding_circle(
CellNumList_setframe_region, 2, 2, close)
surrounding_coordinate_3 = surrounding_circle(
CellNumList_setframe_region, 2, 3, close)
length = len(surrounding_intensity_circle_3)
surrounding = np.zeros((length, 6), dtype=int)
surrounding[0:(len(surrounding_intensity_circle_1)),
0] = surrounding_intensity_circle_1
surrounding[0:(len(surrounding_intensity_circle_2)),
1] = surrounding_intensity_circle_2
surrounding[0:(len(surrounding_intensity_circle_3)),
2] = surrounding_intensity_circle_3
surrounding[0:(len(surrounding_coordinate_1)),
3] = surrounding_coordinate_1
surrounding[0:(len(surrounding_coordinate_2)),
4] = surrounding_coordinate_2
surrounding[0:(len(surrounding_coordinate_3)),
5] = surrounding_coordinate_3
### data output
GroupName = "group1-" + str(GroupNum) + "-inca34-outputs/"
FrameName = "frame" + str(FrameNum)
output_groupfolder = os.path.join(Output_moleParentFolder, GroupName)
## for storing data
if (not (os.path.exists(output_groupfolder))):
os.makedirs(output_groupfolder)
os.chdir(output_groupfolder)
filename = "molecule" + str(MoleculeNum) + "_frame" + str(
FrameNum) + ".txt"
fileid = open(filename, "w")
fileid.write(" ".join([
"intensity1", "intensity2", "intensity3", "coordinate1",
"coordinate2", "coordinate3", "\n"
]))
for line in range(0, length):
line_str = map(str, surrounding[line, :])
line_str.append("\n")
fileid.write(" ".join(line_str))
fileid.close()
print "group", GroupNum, "_frame", FrameNum, "_molecule", MoleculeNum, ": surrounding file created!"
## plotting the frame
mole_start_position = mfc.get_coordinate(CellNumList_setframe[0], ncol)
text_position = [mole_start_position[0] - 15, mole_start_position[1]]
text = "mole_" + str(MoleculeNum)
plt.figure(FrameNum, figsize=(16, 12), dpi=100)
mergeplot = plt.imshow(display_array1)
mergeplot.set_cmap(colormap)
plt.text(text_position[1],
text_position[0],
text,
color="yellow",
size='medium',
weight=400)
plt.colorbar()
mergeplot.set_clim([np.min(display_array3), image_max])
framename_pdf = "molecule" + str(MoleculeNum) + "_frame" + str(
FrameNum) + ".pdf"
framename_png = "molecule" + str(MoleculeNum) + "_frame" + str(
FrameNum) + ".png"
plt.savefig(framename_pdf)
plt.savefig(framename_png)
# plt.show()
plt.close()
## save plots to another folder
output_groupfolder_plot = os.path.join(Output_plotParentFolder,
GroupName)
if (not (os.path.exists(output_groupfolder_plot))):
os.makedirs(output_groupfolder_plot)
framename_pdf_plot = framename_pdf
framename_png_plot = framename_png
shutil.copyfile(
os.path.join(output_groupfolder, framename_pdf),
os.path.join(output_groupfolder_plot, framename_pdf_plot))
shutil.copyfile(
os.path.join(output_groupfolder, framename_png),
os.path.join(output_groupfolder_plot, framename_png_plot))
os.remove(os.path.join(output_groupfolder, framename_pdf))
os.remove(os.path.join(output_groupfolder, framename_png))
else:
print(
"selected region wrong! no pixel of the molecule in this region..")
def simplify_lines_AllFrame(Input_MoleParentFolder_interval, GroupNum,
MoleculeNum, threshold):
fileContents = mfc.read_molecule_files_frominf(
Input_MoleParentFolder_interval, GroupNum, MoleculeNum)
connect_count, frames, cells = mfc.get_frame_count_mole(fileContents)
straightness = []
for FrameNum in frames:
## readin molecule backbone information
fileContents_setframe = mfc.get_content_setframe(
fileContents, FrameNum)
CellNumList_setframe = mfc.get_CellNumbers(fileContents_setframe)
## create a list to store turning points of simplify polyline
list_knots = [0, len(CellNumList_setframe) - 1]
## generate the simplify line
simplify_test = simplify_line_test(CellNumList_setframe, threshold)
while (simplify_test):
## for first recursion
if len(list_knots) == 2:
re_time = [0]
simplify_line(CellNumList_setframe, 0,
len(CellNumList_setframe) - 1, list_knots,
threshold, re_time)
## downstream recursion
else:
## for each segment
for i in range(0, len(list_knots) - 2):
## check whether this segment need more recursion
if simplify_test_list[i]:
re_time = [0]
simplify_line(CellNumList_setframe, list_knots[i],
list_knots[i + 1], list_knots, threshold,
re_time)
list_knots = sorted(list(set(list_knots)))
## check every segment, decide simplify polyline creation is finished or not
simplify_test_list = []
for i in range(0, len(list_knots) - 2):
simplify_test_list.append(
simplify_line_test(
CellNumList_setframe[list_knots[i]:(list_knots[i + 1] +
1)], threshold))
simplify_test = max(simplify_test_list)
## get turning positions
turning_knots_cellnums = list(
np.array(CellNumList_setframe)[list_knots])
## get information related to turning angles
theta_list = angle_list(turning_knots_cellnums)
theta_max = max(map(abs, theta_list))
theta_sum = sum(map(abs, theta_list))
theta_net = sum(theta_list)
## estimation
test_score_sum = float(1 / math.exp((abs(theta_net) + theta_max) / 2))
## result report
straightness.append([FrameNum, theta_net, theta_max, test_score_sum])
return straightness