diff --git a/cal_tools/cal_tools/agipdlib.py b/cal_tools/cal_tools/agipdlib.py
index 019808b84cdfa655bdc615286003c7fbe101301d..9fa3e19a0da721a17d607d61d262708a039321ba 100644
--- a/cal_tools/cal_tools/agipdlib.py
+++ b/cal_tools/cal_tools/agipdlib.py
@@ -67,7 +67,7 @@ def get_acq_rate(fast_paths: Tuple[str, str, int],
     fast_data_file = Path(fast_data_file)
     if fast_data_file.is_file():
         fast_data_path = f'INSTRUMENT/{karabo_id}/DET/{module}CH0:xtdf/image/pulseId'  # noqa
-        with h5py.File(fast_data_file) as fin:
+        with h5py.File(fast_data_file, "r") as fin:
             if fast_data_path in fin:
                 # pulses is of shape (NNNN, 1), of type uint8.
                 # Squeeze out the data, and subtract the 3rd entry from the 2nd
@@ -122,7 +122,7 @@ def get_gain_mode(fname: str, h5path_ctrl: str) -> AgipdGainMode:
 
     h5path_run = h5path_ctrl.replace("CONTROL/", "RUN/", 1)
     h5path_gainmode = f'{h5path_run}/gainModeIndex/value'
-    with h5py.File(fname, 'r') as fd:
+    with h5py.File(fname, "r") as fd:
         if h5path_gainmode in fd:
             return AgipdGainMode(fd[h5path_gainmode][0])
     return AgipdGainMode.ADAPTIVE_GAIN
@@ -289,20 +289,20 @@ class AgipdCorrections:
         data_dict = self.shared_dict[i_proc]
         data_dict['moduleIdx'][0] = module_idx
         try:
-            f = h5py.File(file_name, 'r')
+            f = h5py.File(file_name, "r")
             group = f[agipd_base]["image"]
 
-            (_, first_index, last_index, 
+            (_, first_index, last_index,
              _, valid_indices) = self.get_valid_image_idx(idx_base, f)
 
             allcells = np.squeeze(group['cellId'])
             allpulses = np.squeeze(group['pulseId'])
-         
+
             firange = self.gen_valid_range(first_index, last_index,
                                            self.max_cells, allcells,
                                            allpulses, valid_indices,
                                            apply_sel_pulses)
-                                           
+
             n_img = firange.shape[0]
             data_dict['nImg'][0] = n_img
             if np.all(np.diff(firange) == 1):
@@ -352,7 +352,7 @@ class AgipdCorrections:
             return
         trains = data_dict['trainId'][:n_img]
 
-        with h5py.File(ofile_name, 'w') as outfile:
+        with h5py.File(ofile_name, "w") as outfile:
             # Copy any other data from the input file.
             # This includes indexes, so it's important that the corrected data
             # we write is aligned with the raw data.