def max_distance(celllist):
cell_head = celllist[0]
cell_tail = celllist[len(celllist) - 1]
[y1, x1] = mfc.get_coordinate(cell_head, ncol)
[y2, x2] = mfc.get_coordinate(cell_tail, ncol)
A = y1 - y2
B = x2 - x1
C = x1 * y2 - y1 * x2
coordinates = map(mfc.get_coordinate, celllist,
list(np.repeat(ncol, len(celllist))))
coordinates = np.array(coordinates)
X = list(coordinates[:, 1])
Y = list(coordinates[:, 0])
ds = map(point_to_line_distance, list(np.repeat(A, len(celllist))),
list(np.repeat(B, len(celllist))),
list(np.repeat(C, len(celllist))), X, Y)
max_dis = max(ds)
mid = ds.index(max_dis)
return [max_dis, mid]
def surrounding_OneFrame(Input_MoleParentFolder, Output_moleParentFolder, Output_plotParentFolder, GroupNum, FrameNum, backbone_range = 2, close = False):
GroupNum = int(GroupNum)
FrameNum = int(FrameNum)
GroupFolder = mfc.get_grouppath(GroupNum, Input_MoleParentFolder)
grayData_array = fi.get_grayData_frominf(GroupNum, FrameNum)
display_array = copy.deepcopy(grayData_array)
molecule_filenames = mfc.get_names_setframe(GroupFolder, FrameNum)
molecule_amount = len(molecule_filenames)
start_cells = []
if(molecule_amount):
for molecule_filename in molecule_filenames:
mole_start_cell = surrounding_OneMolecule_forframe(display_array, Input_MoleParentFolder, Output_moleParentFolder, Output_plotParentFolder, GroupNum, FrameNum, 0, backbone_range, close, molecule_filename)
start_cells.append(mole_start_cell)
print "end of frame!"
plt.figure(FrameNum, figsize=(16, 12), dpi = 100)
mergeplot = plt.imshow(display_array)
mergeplot.set_cmap(colormap)
plt.colorbar()
for ind in range(0, molecule_amount):
mole_start_position = mfc.get_coordinate(start_cells[ind], ncol)
text_position = [mole_start_position[0]-15, mole_start_position[1]]
text = molecule_filenames[ind].split(".")[0].split("e")[2]
plt.text(text_position[1], text_position[0], text, color = "yellow", size = 'medium',weight = 400)
mergeplot.set_clim([np.min(display_array), image_max])
else:
plt.figure(1,figsize=(16, 12), dpi = 100)
mergeplot = plt.imshow(display_array)
mergeplot.set_cmap(colormap)
plt.colorbar()
mergeplot.set_clim([np.min(display_array), image_max])
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)
if(not os.path.exists(output_framefolder)):
os.mkdir(output_framefolder)
os.chdir(output_framefolder)
framename_png = "frame" + str(FrameNum) + ".png"
plt.savefig(framename_png)
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.mkdir(output_framefolder_plot)
framename_png_plot = framename_png
shutil.copyfile(os.path.join(output_framefolder,framename_png),os.path.join(output_framefolder_plot,framename_png_plot))
plt.close()
# plt.show()
return molecule_amount
def target_pixel(origin_cellnum, vertical_dis = 0, horizontal_dis = 0): origin_position = mfc.get_coordinate(origin_cellnum, ncol) inframe = 1 target_position = [origin_position[0] + vertical_dis, origin_position[1] + horizontal_dis] target_cellnum = target_position[0]*ncol + target_position[1] if (target_position[0] < 0) or (target_position[0] >= nrow) or (target_position[1] < 0) or (target_position[1] >= ncol): inframe = 0 return [target_cellnum, inframe]
def surrounding_intensity_circle(CellNumList, grayData_array, grayData_surround, backbone_range = 2, surround_range = 1, close = False): surrounding_intensity_circle = [] surrounding_circles = surrounding_circle(CellNumList, backbone_range, surround_range, close) for pixel in surrounding_circles: target_position = list(mfc.get_coordinate(pixel, ncol)) surrounding_intensity_circle.append(get_pixel_intensity(pixel, grayData_array)) grayData_surround[target_position[0], target_position[1]] = mask return surrounding_intensity_circle #, surrounding_origin
def angle_list(turning_knots_cellnums):
if len(turning_knots_cellnums) == 2:
cos_list = [1]
sin_list = [0]
else:
cos_list = []
sin_list = []
for i in range(0, len(turning_knots_cellnums) - 2):
[y1, x1] = mfc.get_coordinate(turning_knots_cellnums[i], ncol)
[y2, x2] = mfc.get_coordinate(turning_knots_cellnums[i + 1], ncol)
[y3, x3] = mfc.get_coordinate(turning_knots_cellnums[i + 2], ncol)
vector1 = [x2 - x1, y2 - y1]
vector2 = [x3 - x2, y3 - y2]
cos_list.append(cosine_distance(vector1, vector2))
sin_list.append(sine_distance(vector1, vector2))
theta_list = map(measure_angle, sin_list, cos_list)
return theta_list
def angle_list(turning_knots_cellnums): if len(turning_knots_cellnums) == 2: cos_list = [1] sin_list = [0] else: cos_list = [] sin_list = [] for i in range(0, len(turning_knots_cellnums) - 2): [y1, x1] = mfc.get_coordinate(turning_knots_cellnums[i], ncol) [y2, x2] = mfc.get_coordinate(turning_knots_cellnums[i + 1], ncol) [y3, x3] = mfc.get_coordinate(turning_knots_cellnums[i + 2], ncol) vector1 = [x2-x1, y2-y1] vector2 = [x3-x2, y3-y2] cos_list.append(cosine_distance(vector1, vector2)) sin_list.append(sine_distance(vector1, vector2)) theta_list = map(measure_angle, sin_list, cos_list) return theta_list
def target_pixel(origin_cellnum, vertical_dis=0, horizontal_dis=0):
origin_position = mfc.get_coordinate(origin_cellnum, ncol)
inframe = 1
target_position = [
origin_position[0] + vertical_dis, origin_position[1] + horizontal_dis
]
target_cellnum = target_position[0] * ncol + target_position[1]
if (target_position[0] < 0) or (target_position[0] >= nrow) or (
target_position[1] < 0) or (target_position[1] >= ncol):
inframe = 0
return [target_cellnum, inframe]
def max_distance(celllist): cell_head = celllist[0] cell_tail = celllist[len(celllist) - 1] [y1, x1] = mfc.get_coordinate(cell_head, ncol) [y2, x2] = mfc.get_coordinate(cell_tail, ncol) A = y1-y2 B = x2-x1 C = x1*y2 - y1*x2 coordinates = map(mfc.get_coordinate, celllist, list(np.repeat(ncol,len(celllist)))) coordinates = np.array(coordinates) X = list(coordinates[:,1]) Y = list(coordinates[:,0]) ds = map(point_to_line_distance, list(np.repeat(A,len(celllist))),list(np.repeat(B,len(celllist))), list(np.repeat(C,len(celllist))), X, Y) max_dis = max(ds) mid = ds.index(max_dis) return [max_dis, mid]
def surrounding_intensity_circle(CellNumList,
grayData_array,
grayData_surround,
backbone_range=2,
surround_range=1,
close=False):
surrounding_intensity_circle = []
surrounding_circles = surrounding_circle(CellNumList, backbone_range,
surround_range, close)
for pixel in surrounding_circles:
target_position = list(mfc.get_coordinate(pixel, ncol))
surrounding_intensity_circle.append(
get_pixel_intensity(pixel, grayData_array))
grayData_surround[target_position[0], target_position[1]] = mask
return surrounding_intensity_circle #, surrounding_origin
def get_pixel_intensity(target_cellnum, grayData_array): target_position = list(mfc.get_coordinate(target_cellnum, ncol)) target_intensity = grayData_array[target_position[0], target_position[1]] return target_intensity
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 get_pixel_intensity(target_cellnum, grayData_array):
target_position = list(mfc.get_coordinate(target_cellnum, ncol))
target_intensity = grayData_array[target_position[0], target_position[1]]
return target_intensity
def surrounding_OneFrame(Input_MoleParentFolder,
Output_moleParentFolder,
Output_plotParentFolder,
GroupNum,
FrameNum,
backbone_range=2,
close=False):
GroupNum = int(GroupNum)
FrameNum = int(FrameNum)
GroupFolder = mfc.get_grouppath(GroupNum, Input_MoleParentFolder)
grayData_array = fi.get_grayData_frominf(GroupNum, FrameNum)
display_array = copy.deepcopy(grayData_array)
molecule_filenames = mfc.get_names_setframe(GroupFolder, FrameNum)
molecule_amount = len(molecule_filenames)
start_cells = []
if (molecule_amount):
for molecule_filename in molecule_filenames:
mole_start_cell = surrounding_OneMolecule_forframe(
display_array, Input_MoleParentFolder, Output_moleParentFolder,
Output_plotParentFolder, GroupNum, FrameNum, 0, backbone_range,
close, molecule_filename)
start_cells.append(mole_start_cell)
print "end of frame!"
plt.figure(FrameNum, figsize=(16, 12), dpi=100)
mergeplot = plt.imshow(display_array)
mergeplot.set_cmap(colormap)
plt.colorbar()
for ind in range(0, molecule_amount):
mole_start_position = mfc.get_coordinate(start_cells[ind], ncol)
text_position = [
mole_start_position[0] - 15, mole_start_position[1]
]
text = molecule_filenames[ind].split(".")[0].split("e")[2]
plt.text(text_position[1],
text_position[0],
text,
color="yellow",
size='medium',
weight=400)
mergeplot.set_clim([np.min(display_array), image_max])
else:
plt.figure(1, figsize=(16, 12), dpi=100)
mergeplot = plt.imshow(display_array)
mergeplot.set_cmap(colormap)
plt.colorbar()
mergeplot.set_clim([np.min(display_array), image_max])
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)
if (not os.path.exists(output_framefolder)):
os.mkdir(output_framefolder)
os.chdir(output_framefolder)
framename_png = "frame" + str(FrameNum) + ".png"
plt.savefig(framename_png)
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.mkdir(output_framefolder_plot)
framename_png_plot = framename_png
shutil.copyfile(os.path.join(output_framefolder, framename_png),
os.path.join(output_framefolder_plot, framename_png_plot))
plt.close()
# plt.show()
return molecule_amount
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..")