def pd_read_csv_data_from_dir(self, input_dir, extension_str='.csv'):
'''
Input:
input_dir: '/input/dir'
Output:
feature_ary = np.array
data_x = np.array
data_y = np.array
'''
file_obj = FileList()
file_ary = file_obj.find_file(input_dir, extension_str)
df_list = []
for temp_file in file_ary:
temp_df = self.pd_read_csv_data(temp_file)
df_list.append(temp_df)
result_df = pd.concat(df_list, axis=0)
## reset all index
result_df = result_df.set_index(np.arange(result_df.shape[0]))
return result_df
def get_csv_data_from_dir(self,
input_dir,
outcome_index=26,
extension_str='.csv'):
'''
Input:
input_dir: '/input/dir'
Output:
feature_ary = np.array
data_x = np.array
data_y = np.array
'''
file_obj = FileList()
file_ary = file_obj.find_file(input_dir, extension_str)
data_x = []
data_y = []
data_x = np.array(data_x)
data_y = np.array(data_y)
for temp_index, temp_file in enumerate(file_ary):
features_ary, temp_data_x, temp_data_y = self.read_csv_data(
temp_file, outcome_index)
if temp_index == 0:
data_x = temp_data_x
data_y = temp_data_y
else:
data_x = np.concatenate((data_x, temp_data_x), axis=0)
data_y = np.concatenate((data_y, temp_data_y), axis=0)
print(temp_file)
print(len(temp_data_x))
print(len(data_x))
return features_ary, data_x, data_y
def gpr_file_test():
file_path_ary = [
'/home/ryan/smb_data/CytoOneArray/RD/完成報告',
'/home/ryan/smb_data/CytoOneArray/RD/審查中報告',
'/home/ryan/smb_data/brank_data/For Brank/GPR'
]
# file_path_ary = ["/home/ryan/smb_data/brank_data/For Brank/GPR"]
# file_path = '/home/ryan/smb_data/CytoOneArray/RD/完成報告/華聯/2014'
file_ext = 'gpr'
gpr_file_list = '/home/ryan/src_dir/CytoOA_AI/data/gpr_file_list.txt'
missing_file_list = '/home/ryan/src_dir/CytoOA_AI/data/missing_file_list.txt'
match_file_list = '/home/ryan/src_dir/CytoOA_AI/data/match_file_list.txt'
file_obj = FileList()
file_ary = []
for file_path in file_path_ary:
file_ary += file_obj.find_file(file_path, file_ext)
fh_writer = open(gpr_file_list, 'w')
fh_missing = open(missing_file_list, 'w')
fh_match = open(match_file_list, 'w')
all_id = []
array_id_2_path_dict = {}
for temp_file in file_ary:
# print(temp_file)
fh_writer.write(temp_file + "\n")
file_name = file_obj.get_gpr_code(temp_file)
# print(file_name)
### recording array id to file path
array_id_2_path_dict[file_name[0]] = temp_file
all_id += file_name
fh_writer.close()
# print(all_id)
gpr_id_dict = list_2_dict(all_id)
###
excel_reader = ExcelReader()
input_file = '/home/ryan/src_dir/CytoOA_AI/data/Cyto_Report_summary2.xlsx'
# input_file = '/home/ryan/src_dir/CytoOA_AI/data/Cyto_Report_summary.xls'
excel_df = excel_reader.read_excel(input_file)
excel_gpr_id = get_gpr_id_from_excel_df(excel_df)
excel_grp_dict = list_2_dict(excel_gpr_id)
hit_count = 0
miss_count = 0
total_count = 0
miss_id = []
for key, value in excel_grp_dict.items():
if key in gpr_id_dict:
hit_count += 1
fh_match.write(str(key) + "\t" + array_id_2_path_dict[key] + "\n")
else:
miss_count += 1
miss_id.append(key)
fh_missing.write(str(key) + "\n")
total_count += 1
print("Missing id = ")
print(miss_id)
print("Hit count = {}".format(hit_count))
print("Miss_count = {}".format(miss_count))
print("Total_count = {}".format(total_count))
fh_writer.close()
fh_missing.close()
fh_match.close()
