def create_condit_dict(self):
"""takes pmap_path, opens it and turns it into condit_dict (conditions dict)"""
# open plate map and get headings
pmap_rows = mia.csv_to_arr(self.pmap_path)
col_headings = pmap_rows[0][1:]
del pmap_rows[0]
pmap_cols = mia.rotate(pmap_rows)
row_headings = pmap_cols[0]
del pmap_cols[0]
pmap_cols = delete_empty_arrs(pmap_cols, col_headings, blank='')
pmap_rows = mia.rotate(pmap_cols)
pmap_rows = delete_empty_arrs(pmap_rows, row_headings, blank='')
pmap_cols = mia.rotate(pmap_rows)
# make dict keys
condit_dict = {}
for row in pmap_rows:
for item in row:
condit_dict[item] = []
# put in values
for r in range(len(pmap_rows)):
for c in range(len(pmap_rows[r])):
well_name = (row_headings[r] + double_digits(col_headings[c]))
condit_dict[pmap_rows[r][c]].append(well_name)
self.pmap_rows = pmap_rows
self.condit_index = sorted(condit_dict.keys())
return condit_dict
def make_cells(self):
"""
in progress, makes cells
need to refactor all of well class
"""
try:
col_del_num = self.col_headings.index(" ")
except ValueError: #use 'in' to do this instead
col_del_num = -1
if col_del_num > -1:
del self.cols[col_del_num]
del self.col_headings[col_del_num]
cell_col_num = self.col_headings.index(self.cell_col_h)
self.row_headings = self.cols[cell_col_num]
del self.cols[cell_col_num]
del self.col_headings[cell_col_num]
self.rows = mia.rotate(self.cols)
cell_ids = sorted(set(self.row_headings))
cell_dict = {}
for cell_id in cell_ids:
cell_dict[cell_id] = []
for i, rh in enumerate(self.row_headings):
cell_dict[rh].append(self.rows[i])
self.cells = []
for id_num, rows in cell_dict.items():
self.cells.append(
cell(id_num, self.condition, self, rows,
copy.copy(self.col_headings)))
def __init__(self, condition, name) :
""" well constructor """
self.condition = condition
self.plate = self.condition.plate
self.name = name
self.path = (self.plate.path + self.plate.name
+ "_" + self.name + ".csv")
self.rows = mia.csv_to_arr(self.path)
for i, item in enumerate(self.rows[0]):
self.rows[0][i] = spec_encode(item)
self.col_headings = self.rows[0]
del self.rows[0]
self.cols = mia.rotate(self.rows)
self.cell_col_h = "Track n°"
self.cell_col_h = spec_encode(self.cell_col_h)
self.make_cells()
def make_avg_col(self):
#mia.print_types(self.all_dist_cols)
dist_rows = mia.rotate(self.all_dist_cols)
avg_col = []
for row in dist_rows:
#try :
avg_col.append(mia.calc_avg(row))
#except TypeError :
#print("condition = {0}, row = {1}".format(self.name,row))
#if self.plate.except_count == 0 :
#print(self.name)
#mia.print_arr(dist_rows)
#self.plate.except_count+=1
return avg_col
def __init__(self, id_num, condition, well, rows, col_headings):
""" cell constructor """
self.id_num = id_num
self.condition = condition
self.well = well
self.rows = rows
self.col_headings = col_headings
self.cols = mia.rotate(rows)
x_i = self.col_headings.index("X")
y_i = self.col_headings.index("Y")
self.x_col = self.cols[x_i]
self.y_col = self.cols[y_i]
self.dist_col = self.make_dist_col()
def print_to_csv(self):
rows = mia.rotate(self.all_condit_cols)
mia.arr_to_csv(rows, self.out_path, mode="w")
def print_to_csv(self):
self.out_path = self.make_out_path()
rows = mia.rotate(self.all_dist_cols)
mia.arr_to_csv(rows, self.out_path, mode="w")
