def surrounding_circle(CellNumList,backbone_range = 2, surround_range = 1, close = False): vertical_range = backbone_range + surround_range horizontal_range = vertical_range surrounding_condition = ventral_dorsal_string(CellNumList, vertical_range) if(close): head_cells, tail_cells = mfc.boundary_x(ncol, CellNumList) for head in head_cells: head_box = head_tail_box(head, True, False, vertical_range, horizontal_range) for head_pixel in head_box: surrounding_condition.append(head_pixel) for tail in tail_cells: tail_box = head_tail_box(tail, False, True, vertical_range, horizontal_range) for tail_pixel in tail_box: surrounding_condition.append(tail_pixel) surrounding_condition = set(map(tuple, surrounding_condition)) surrounding_condition = list(map(list, surrounding_condition)) surrounding_condition = np.array(surrounding_condition) surrounding_inframe = surrounding_condition[:,1] surrounding_circle = surrounding_condition.compress(surrounding_inframe, axis = 0)[:,0] ### origin_backbone = surrounding_condition.compress(surrounding_inframe, axis = 0)[:,[0,2]] ### ready to output the origin position(cellnums)? return list(surrounding_circle) #list(surrounding_origin)
def surrounding_circle(CellNumList,
backbone_range=2,
surround_range=1,
close=False):
vertical_range = backbone_range + surround_range
horizontal_range = vertical_range
surrounding_condition = ventral_dorsal_string(CellNumList, vertical_range)
if (close):
head_cells, tail_cells = mfc.boundary_x(ncol, CellNumList)
for head in head_cells:
head_box = head_tail_box(head, True, False, vertical_range,
horizontal_range)
for head_pixel in head_box:
surrounding_condition.append(head_pixel)
for tail in tail_cells:
tail_box = head_tail_box(tail, False, True, vertical_range,
horizontal_range)
for tail_pixel in tail_box:
surrounding_condition.append(tail_pixel)
surrounding_condition = set(map(tuple, surrounding_condition))
surrounding_condition = list(map(list, surrounding_condition))
surrounding_condition = np.array(surrounding_condition)
surrounding_inframe = surrounding_condition[:, 1]
surrounding_circle = surrounding_condition.compress(surrounding_inframe,
axis=0)[:, 0]
### origin_backbone = surrounding_condition.compress(surrounding_inframe, axis = 0)[:,[0,2]]
### ready to output the origin position(cellnums)?
return list(surrounding_circle) #list(surrounding_origin)
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(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..")
