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_OneGroup(Input_MoleParentFolder, Output_moleParentFolder, Output_plotParentFolder, GroupNum, backbone_range = 2, close = False): GroupNum = int(GroupNum) GroupFolder = mfc.get_grouppath(GroupNum, Input_MoleParentFolder) framenames = fi.get_framenames(GroupNum) for FrameNum in range(0, len(framenames)): print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ for frame ", FrameNum, "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" surrounding_OneFrame(Input_MoleParentFolder, Output_moleParentFolder, Output_plotParentFolder, GroupNum, FrameNum, backbone_range, close) print "end of group!"
def surrounding_OneGroup(Input_MoleParentFolder,
Output_moleParentFolder,
Output_plotParentFolder,
GroupNum,
backbone_range=2,
close=False):
GroupNum = int(GroupNum)
GroupFolder = mfc.get_grouppath(GroupNum, Input_MoleParentFolder)
framenames = fi.get_framenames(GroupNum)
for FrameNum in range(0, len(framenames)):
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ for frame ", FrameNum, "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
surrounding_OneFrame(Input_MoleParentFolder, Output_moleParentFolder,
Output_plotParentFolder, GroupNum, FrameNum,
backbone_range, close)
print "end of group!"
def Effected_OneMolecule(Input_MoleParentFolder_interval, Input_SurroundingParentFolder_interval, GroupNum, MoleculeNum, layer, threshold):
#def main(argv):
# try:
# opts, args = getopt.getopt(argv, "hs:e:", ["help", "grammar="])
# except getopt.GetoptError:
# usage()
# sys.exit(2)
# GroupNum = int(args[0])
# MoleculeNum = int(args[1])
# layer = int(args[2])
GroupNum = int(GroupNum)
MoleculeNum = int(MoleculeNum)
layer = int(layer)
print GroupNum, MoleculeNum
GroupName = "group1-" + str(GroupNum) + "-inca34-outputs/"
GroupFolder = mfc.get_grouppath(GroupNum, Input_MoleParentFolder_interval)
if os.path.exists(GroupFolder):
molecule_fileContents = mfc.read_molecule_files_frominf(Input_MoleParentFolder_interval, GroupNum, MoleculeNum)
connect_count, frames, cells = mfc.get_frame_count_mole(molecule_fileContents)
for frame in frames:
BackbonefileContents = mfc.get_content_setframe(molecule_fileContents, frame)
FrameNum = frame
surrounding_fileName = "molecule" + str(MoleculeNum) + "_frame" + str(FrameNum) + ".txt"
SurroundingReadPath = os.path.join(Input_SurroundingParentFolder_interval, GroupName, surrounding_fileName)
SurrID = open(SurroundingReadPath, 'r')
SurroundingfileContents = SurrID.readlines()
ConditionList = determine_within_forbackbone(BackbonefileContents, SurroundingfileContents, layer, threshold)
## plotting
fig = plt.figure(frame)
BackboneIntensity = mfc.get_IntenAll(BackbonefileContents)
attention_x = list(map(multiply, range(0, len(BackboneIntensity)), ConditionList))
attention_x = filter(lambda x:x is not 0, attention_x)
if ConditionList[0] != 0:
attention_x.insert(0, 0)
attention_y = map(multiply, BackboneIntensity, ConditionList)
if attention_y.count(0) != 0:
attention_y = filter(lambda y:y is not 0, attention_y)
line, = plt.plot(BackboneIntensity, label = "intensity porfile")
dot, = plt.plot(attention_x, attention_y, "ro", color = "red")
Title = "Group" + str(GroupNum) + "_Molecule" + str(MoleculeNum) + " Backbone1 intensity" + "(default threshold" + str(threshold) + ")"
plt.title(Title)
plt.xlabel("position(orientation depend on alignment)/pixels")
plt.ylabel("intensity")
# plt.legend([line], "intensity porfile", loc = 4)
plt.legend([line, dot], ["intensity porfile", "effected pixels(from layer"+str(layer) + ")"])
# print ConditionList
plt.show()
else:
print "group not exist!"
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 Effected_OneMolecule(Input_MoleParentFolder_interval,
Input_SurroundingParentFolder_interval, GroupNum,
MoleculeNum, layer, threshold):
#def main(argv):
# try:
# opts, args = getopt.getopt(argv, "hs:e:", ["help", "grammar="])
# except getopt.GetoptError:
# usage()
# sys.exit(2)
# GroupNum = int(args[0])
# MoleculeNum = int(args[1])
# layer = int(args[2])
GroupNum = int(GroupNum)
MoleculeNum = int(MoleculeNum)
layer = int(layer)
print GroupNum, MoleculeNum
GroupName = "group1-" + str(GroupNum) + "-inca34-outputs/"
GroupFolder = mfc.get_grouppath(GroupNum, Input_MoleParentFolder_interval)
if os.path.exists(GroupFolder):
molecule_fileContents = mfc.read_molecule_files_frominf(
Input_MoleParentFolder_interval, GroupNum, MoleculeNum)
connect_count, frames, cells = mfc.get_frame_count_mole(
molecule_fileContents)
for frame in frames:
BackbonefileContents = mfc.get_content_setframe(
molecule_fileContents, frame)
FrameNum = frame
surrounding_fileName = "molecule" + str(
MoleculeNum) + "_frame" + str(FrameNum) + ".txt"
SurroundingReadPath = os.path.join(
Input_SurroundingParentFolder_interval, GroupName,
surrounding_fileName)
SurrID = open(SurroundingReadPath, 'r')
SurroundingfileContents = SurrID.readlines()
ConditionList = determine_within_forbackbone(
BackbonefileContents, SurroundingfileContents, layer,
threshold)
## plotting
fig = plt.figure(frame)
BackboneIntensity = mfc.get_IntenAll(BackbonefileContents)
attention_x = list(
map(multiply, range(0, len(BackboneIntensity)), ConditionList))
attention_x = filter(lambda x: x is not 0, attention_x)
if ConditionList[0] != 0:
attention_x.insert(0, 0)
attention_y = map(multiply, BackboneIntensity, ConditionList)
if attention_y.count(0) != 0:
attention_y = filter(lambda y: y is not 0, attention_y)
line, = plt.plot(BackboneIntensity, label="intensity porfile")
dot, = plt.plot(attention_x, attention_y, "ro", color="red")
Title = "Group" + str(GroupNum) + "_Molecule" + str(
MoleculeNum
) + " Backbone1 intensity" + "(default threshold" + str(
threshold) + ")"
plt.title(Title)
plt.xlabel("position(orientation depend on alignment)/pixels")
plt.ylabel("intensity")
# plt.legend([line], "intensity porfile", loc = 4)
plt.legend([line, dot], [
"intensity porfile",
"effected pixels(from layer" + str(layer) + ")"
])
# print ConditionList
plt.show()
else:
print "group not exist!"
