def normal():
wanted = json.loads(open("wanted.json").read())
original_path = os.path.abspath(os.getcwd())
for d, v in wanted.items():
for subdir, lins in v.items():
path = os.path.abspath(os.path.join(d, subdir))
print("Processing path:", path)
os.chdir(path)
for lin in lins:
lineage_num = int(lin)
target_file = os.path.join(
"data",
"cell_lines",
"lineage{0:02d}.npy".format(lineage_num)
)
cell_line = np.load(target_file)
spot_plot.plot_images(cell_line, lineage_num)
try:
spot_plot.plot_graphs(cell_line, lineage_num)
except AttributeError:
print("ParA data missing")
get_parA.main()
cell_line = np.load(target_file)
spot_plot.plot_graphs(cell_line, lineage_num)
print("Generated plots for lineage {0}".format(lineage_num))
os.chdir(original_path)
def end(self, discard=False):
if discard:
plt.close()
return
# backup previous lineage file
previous_file = "data/cell_lines/lineage{0:02d}.npy".format(self.lineage_num)
if os.path.exists(previous_file):
if not os.path.exists("data/cell_lines/backups"):
os.mkdir("data/cell_lines/backups")
backup_file = "data/cell_lines/backups/{0}-lineage{1:02d}.npy".format(
datetime.datetime.strftime(datetime.datetime.now(), "%Y%m%d-%H%M"),
self.lineage_num
)
attempt = 2
while os.path.exists(backup_file):
first = backup_file.split(".npy")[0]
backup_file = "{0}.npy-{1}".format(first, attempt)
attempt += 1
print("Backing up previous lineage file to {0}".format(backup_file))
os.rename(previous_file, backup_file)
print("Saving new lineage file")
np.save(
"data/cell_lines/lineage{0:02d}".format(self.lineage_num),
self.cell_line
)
if self.GEN_PLOTS:
print("Saving new PDFs")
spot_plot.plot_images(self.cell_line, int(self.lineage_num))
spot_plot.plot_graphs(self.cell_line, int(self.lineage_num), um=True)
spot_spread.gen_xl(self.cell_line, int(self.lineage_num))
plt.close(self.fig)