replace print with logging

mesmerize/analysis/data_types.py

@@ -27,6 +27,10 @@
 from ..common.configuration import get_environment
 from tqdm import tqdm
 from functools import lru_cache
+import logging
+
+
+logger = logging.getLogger()
 
 
 class _HistoryTraceExceptions(Exception):
@@ -591,14 +595,14 @@ def from_proj(cls, proj_path: str, dataframe: pd.DataFrame, sub_dataframe_name:
 
         """
         df = dataframe.copy()
-        print('Collecting image metadata')
+        logger.info('Collecting image metadata')
         tqdm().pandas()
         df[['meta', 'stim_maps']] = df.progress_apply(lambda r: Transmission._load_files(proj_path, r), axis=1)
 
         Transmission._load_imginfo.cache_clear()
 
         try:
-            print('Collecting curve data')
+            logger.info('Collecting curve data')
             df['_RAW_CURVE'] = df['ROI_State'].progress_apply(
                     lambda r: r['curve_data'][1]
                 )
@@ -608,7 +612,7 @@ def from_proj(cls, proj_path: str, dataframe: pd.DataFrame, sub_dataframe_name:
                              "the project dataframe where the curve data are missing")
 
         try:
-            print('Collecting curve data')
+            logger.info('Collecting curve data')
             df['_SPIKES'] = df['ROI_State'].progress_apply(
                 lambda r: r['spike_data'][1] if (r['spike_data'] is not None) else None
             )
@@ -617,7 +621,7 @@ def from_proj(cls, proj_path: str, dataframe: pd.DataFrame, sub_dataframe_name:
             warn('spikes or data not found, probably is probably from Mesmerize version < 0.2')
 
         try:
-            print('Collecting dfof data')
+            logger.info('Collecting dfof data')
             df['_DFOF'] = df['ROI_State'].progress_apply(
                 lambda r: r['dfof_data'][1] if (r['dfof_data'] is not None) else None
             )

mesmerize/common/qdialogs.py

@@ -50,7 +50,17 @@ def fn(self, *args, **kwargs):
                 return func(self, *args, **kwargs)
             except Exception as e:
                 tb = traceback.format_exc()
-                args = (self, title, msg + f'\n\n{e.__class__.__name__}: {e}\n\n{tb}', QMessageBox.Ok)
+                args = \
+                    (
+                        self,
+                        title,
+                        msg +\
+                        f'\n\n'
+                        f'{e.__class__.__name__}: {e}'
+                        f'\n\n{tb}',
+                        QMessageBox.Ok,
+                        QMessageBox.Information
+                    )
                 if help_func is not None and QMessageBox.warning(*args, QMessageBox.Help) == QMessageBox.Help:
                     help_func(e, tb)
                 else:

mesmerize/pyqtgraphCore/flowchart/library/common.py

@@ -22,6 +22,10 @@
 from ...widgets.KwargPlainTextEdit import KwargPlainTextEdit
 from ....analysis import organize_dataframe_columns
 # from PyQt5.QtWidgets import QLineEdit as LineEdit
+import logging
+
+
+logger = logging.getLogger()
 
 
 def generateUi(opts):
@@ -181,7 +185,7 @@ def changed(self):
         self.sigStateChanged.emit(self)
         out = f"Processing node: {self.name()}\n"
 
-        sys.stdout.write(out)
+        logger.info(out)
 
     def process(self, **kwargs):#In, display=True):
         In = kwargs['In']

mesmerize/viewer/core/viewer_work_environment.py

@@ -23,6 +23,10 @@
 from uuid import uuid4
 from uuid import UUID as UUID_type
 from typing import Optional, Tuple
+import logging
+
+
+logger = logging.getLogger()
 
 
 class ViewerWorkEnv:
@@ -136,7 +140,7 @@ def clear(self):
         self.origin_file = ''
         self._saved = True
         self.changed_items = []
-        print('Work environment dumped!')
+        logger.info('Work environment dumped!')
 
     def restore_rois_from_states(self):
         if (self.roi_manager is not None) and (self.roi_states is not None):

mesmerize/viewer/main_window.py

@@ -37,6 +37,10 @@
 import pandas as pd
 from typing import Optional, Union
 from uuid import UUID as UUID_type
+import logging
+
+
+logger = logging.getLogger()
 
 _custom_modules_dir = configuration.get_sys_config()['_MESMERIZE_CUSTOM_MODULES_DIR']
 _custom_modules_package_name = os.path.basename(os.path.dirname(_custom_modules_dir))
@@ -344,7 +348,7 @@ def open_workEnv_editor(self):
         try:
             changes = objecteditor.oedit(self.vi.viewer.workEnv)
         except:
-            print(traceback.format_exc())
+            logger.info((traceback.format_exc()))
             # QtWidgets.QMessageBox.de(self, 'Unable to open work environment editor',
             #                               'The following error occured while trying to open the work environment editor:'
             #                               '\n', traceback.format_exc())

mesmerize/viewer/modules/batch_manager.py

@@ -49,13 +49,18 @@
 elif IS_WINDOWS:
     from win32api import TerminateProcess, CloseHandle
 
+import logging
+
+
+logger = logging.getLogger()
+
 
 class ModuleGUI(QtWidgets.QWidget):
     """GUI for the Batch Manager"""
     listwchanged = QtCore.pyqtSignal()
 
     def __init__(self, parent, run_batch: list = None, testing: bool = False):
-        print('starting batch mananger')
+        logger.info('starting batch mananger')
         QtWidgets.QWidget.__init__(self, parent)
         self._testing = testing
         self.ui = Ui_Form()
@@ -157,7 +162,7 @@ def init_batch(self, run_batch):
                     return
             else:
                 path = run_batch[0]
-                print('Opening batch: ' + path)
+                logger.info('Opening batch: ' + path)
 
             dfpath = os.path.join(path, 'dataframe.batch')
             if os.path.isfile(dfpath):
@@ -171,7 +176,7 @@ def init_batch(self, run_batch):
         self.set_workdir(True)  # does a check to see if the workdir is writable upon batch manager initiation
 
         if run_batch is not None:
-            print('Running from item ' + run_batch[1])
+            logger.info('Running from item ' + run_batch[1])
             # ix = self.df.index[self.df['uuid'] == uuid.UUID(run_batch[1])]
             # i = int(ix.to_native_types()[0])
             i = self.get_item_index(run_batch[1])

mesmerize/viewer/modules/caiman_dfof.py

@@ -18,6 +18,10 @@
 from .roi_manager_modules.managers import ManagerCNMFROI, ManagerVolCNMF, ManagerVolMultiCNMFROI
 import numpy as np
 from tqdm import tqdm
+import logging
+
+
+logger = logging.getLogger()
 
 
 # just need the function signature
@@ -162,7 +166,7 @@ def _set_data_multi2d(
 
         dfofs = np.vstack(roi_manager.cnm_dfof)
 
-        print(
+        logger.info(
             f"dfof shape:\t{dfofs.shape}\n"
             f"roi_list len:\t{len(roi_manager.roi_list)}"
         )

mesmerize/viewer/modules/caiman_motion_correction.py

@@ -26,6 +26,10 @@
 from math import ceil
 from itertools import product
 from typing import *
+import logging
+
+
+logger = logging.getLogger()
 
 
 class ModuleGUI(QtWidgets.QDockWidget):
@@ -219,7 +223,7 @@ def view_output_projections(self):
 
         proj = self.ui.comboBoxProjectionsOption.currentText()
 
-        print("Calculating projections, please wait...")
+        logger.info("Calculating projections, please wait...")
 
         self.currrent_projections = Parallel(n_jobs=cpu_count(), verbose=5)(
             delayed(ModuleGUI._get_projection)(proj, batch_path, item_uuid) for item_uuid in item_uuids
@@ -233,7 +237,7 @@ def plot_output_projections(self):
         if self.currrent_projections is None:
             raise AttributeError("Projections not calculated")
 
-        print("Plotting projections")
+        logger.info("Plotting projections")
         if self.projections_plot_widget is None:
             self.projections_plot_widget = MatplotlibWidget()
         else:

mesmerize/viewer/modules/cnmf.py

@@ -20,6 +20,10 @@
 from shutil import copy
 import os
 from copy import deepcopy
+import logging
+
+
+logger = logging.getLogger()
 
 
 class ModuleGUI(QtWidgets.QDockWidget):
@@ -197,7 +201,7 @@ def add_to_batch(self, params: dict = None) -> UUID:
             return
 
         if d['use_seeds']:
-            print("Copying component seed file")
+            logger.info("Copying component seed file")
             copy(seed_path, os.path.join(batch_manager.batch_path, f'{u}.ain'))
 
         self.vi.viewer.status_bar_label.showMessage('Done adding CNMF: ' + name + ' to batch!')

mesmerize/viewer/modules/cnmf_3d.py

@@ -18,6 +18,10 @@
 from shutil import copy
 import os
 from copy import deepcopy
+import logging
+
+
+logger = logging.getLogger()
 
 
 class ModuleGUI(QtWidgets.QDockWidget):
@@ -196,7 +200,7 @@ def add_to_batch(self, params: dict = None) -> UUID:
             return
 
         if d['use_seeds']:
-            print("Copying component seeds files")
+            logger.info("Copying component seeds files")
             copy(seed_path, os.path.join(bm.batch_path, f'{u}.ain'))
 
         if d['keep_memmap']:

mesmerize/viewer/modules/exporter.py

@@ -7,6 +7,10 @@
 import os
 import skvideo.io
 from .pytemplates.exporter_pytemplate import *
+import logging
+
+
+logger = logging.getLogger()
 
 
 # adapted from https://github.com/ver228/tierpsy-tracker/blob/master/tierpsy/analysis/compress/compressVideo.py
@@ -81,7 +85,7 @@ def export(self):
 
         seq = self.viewer.workEnv.imgdata.seq
 
-        print('Normalizing image for 8bit video output')
+        logger.info('Normalizing image for 8bit video output')
         norm = normalize_image(seq, vmin, vmax)
 
         # RGB LUT
@@ -103,10 +107,10 @@ def export(self):
                 '-filter:v': f"setpts={pts}*PTS",
                 '-vcodec': codec
             }
-        print("Creating ffmpeg writer")
+        logger.info("Creating ffmpeg writer")
         writer = skvideo.io.FFmpegWriter(f'{path}.{extn}', outputdict=output_params)
 
-        print("Writing video")
+        logger.info("Writing video")
         for i in tqdm(range(norm.shape[2])):
             frame = norm[:, :, i]
             # use the LUT to create RGB pseudocolored image