# Path: src/plugins/util/plugin.py
# class PluginDefault:
#     def __init__(self, widget, widget_labels_class, name):
#         self.name = name
#         self.widget = widget
#         if hasattr(self.widget, 'project') and hasattr(self.widget, 'plugin_position'):
#             self.widget.params = self.widget.project.pipeline[self.widget.plugin_position]
#         self.widget_labels = widget_labels_class
# 
#     def run(self, input_paths=None):
#         return self.widget.execute_primary_function(input_paths)
# 
#     def get_input_paths(self):
#         return self.widget.selected_videos
# 
#     def output_number_expected(self, expected_input_number=None):
#         if expected_input_number:
#             return expected_input_number
#         else:
#             return len(self.get_input_paths())
# 
#     def check_ready_for_automation(self, expected_input_number):
#         return False
# 
#     def automation_error_message(self):
#         return "Plugin " + self.name + " is not suitable for automation."
# 
# Path: src/plugins/util/file_io.py
# class UnknownFileFormatError(Exception):
# def load_npy(filename, progress_callback=None, segment=None):
# def get_name_after_no_overwrite(name_before, manip, project):
# def save_file(path, data):
# def load_file(filename, progress_callback=None, segment=None):
# def load_reference_frame_npy(filename, offset):
# def load_reference_frame(filename, offset=0):
# 
# Path: src/plugins/util/fileconverter.py
# class RawToNpyConvertError(Exception):
#   def error_msg(self):
# def tif2npy(filename_from, filename_to, progress_callback):
# def raw2npy(filename_from, filename_to, dtype, width, height, num_channels, channel, progress_callback,
#             ignore_shape_error=False):
# 
# Path: src/plugins/util/custom_qt_items.py
# class JSObjectModel(QAbstractTableModel):
# class FileTableModel(JSObjectModel):
# class FileTable(QTableView):
# class ImageStackListView(QListView):
# class MyProgressDialog(QProgressDialog):
# class InfoWidget(QFrame):
# class MyListView(QListView):
# class RoiModel(QStandardItemModel):
# class RoiItemModel(QAbstractListModel):
# class RoiList(QListView):
#     class Labels(object):
#     class Defaults(object):
# class WarningWidget(QFrame):
# class CheckableComboBox(QtGui.QComboBox):
# class MyTableWidget(QTableWidget):
# class PlayerDialog(QDialog):
#   def __init__(self, data, parent=None):
#   def rowCount(self, parent):
#   def columnCount(self, parent): 
#   def data(self, index, role):
#   def headerData(self, section, orientation, role):
#   def retrieve(self, row, key=None):
#   def __init__(self, data, parent=None):
#   def get_path(self, index):
#   def get_entry(self, index):
#   def __init__(self, project=None, parent=None):
#   def selected_paths(self):
#     def __init__(self, parent=None):
#     def contextMenuEvent(self, event):
#   def __init__(self, title, desc, parent=None):
#   def __init__(self, text, parent=None):
#   def setup_ui(self, text):
#   def __init__(self, parent=None):
#   def currentChanged(self, current, previous):
#   def __init__(self, parent=None):
#   def supportedDropActions(self):
#   def dropMimeData(self, data, action, row, column, parent):
#   def flags(self, index):
#   def removeRows(self, row, count, parent):
#   def insertRows(self, row, count, parent):
#     def __init__(self, parent=None):
#     def appendRoi(self, name):
#     def edit_roi_name(self, name, index):
#     def rowCount(self, parent):
#     def data(self, index, role):
#     def setData(self, index, value, role):
#     def flags(self, index):
#     def removeRow(self, roi_to_remove):
#     def __init__(self, widget, roi_types, standard_model=False):
#     def selected_roi_changed(self, selection):
#     def remove_all_rois(self):
#     def setup_params(self, reset=False):
#     def setup_param_signals(self):
#     def prepare_roi_list_for_update(self, selected, deselected):
#     def __init__(self, text, parent=None):
#     def setup_ui(self, text):
#     def __init__(self):
#     def handleItemPressed(self, index):
#   def __init__(self, data=None, *args):
#   def setmydata(self):
#   def update(self, data):
#   def __init__(self, project, filename, parent=None, scaling=True):
#   def show_frame(self, frame_num):
#   def setup_ui(self):
#   def slider_moved(self, value):


import functools
import os
import sys
import traceback
import numpy as np
import psutil
import qtutil
import tifffile as tiff
from shutil import copyfile
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from .util.plugin import PluginDefault
from .util import file_io, fileconverter
from .util import custom_qt_items as cqt

    try:
      fileconverter.tif2npy(filename, path, callback)
    except:
      qtutil.critical('Converting tiff to npy failed.')
      progress.close()
    else:
      ret_filename = path
      with tiff.TiffFile(filename) as tif:
        if rescale_value != 1.00:
          w, h = tif[0].shape
          rescale_width = int(w * rescale_value)
          rescale_height = int(h * rescale_value)
          no_frames = len(tif)
          unscaled = np.load(path)
          try:
            scaled = self.bin_ndarray(unscaled, (no_frames, rescale_height,
                                        rescale_width), callback, operation='mean')
            np.save(path, scaled)
          except:
            qtutil.critical('Rebinning tiff failed. We can only scale down from larger sized files to preserve data')
            progress.close()
    return ret_filename

  def to_npy(self, filename):
    if filename.endswith('.raw'):
      filename = self.convert_raw(filename)
    elif filename.endswith('.tif'):
      filename = self.convert_tif(filename)
    else:

# Path: src/plugins/util/plugin.py
# class PluginDefault:
#     def __init__(self, widget, widget_labels_class, name):
#         self.name = name
#         self.widget = widget
#         if hasattr(self.widget, 'project') and hasattr(self.widget, 'plugin_position'):
#             self.widget.params = self.widget.project.pipeline[self.widget.plugin_position]
#         self.widget_labels = widget_labels_class
# 
#     def run(self, input_paths=None):
#         return self.widget.execute_primary_function(input_paths)
# 
#     def get_input_paths(self):
#         return self.widget.selected_videos
# 
#     def output_number_expected(self, expected_input_number=None):
#         if expected_input_number:
#             return expected_input_number
#         else:
#             return len(self.get_input_paths())
# 
#     def check_ready_for_automation(self, expected_input_number):
#         return False
# 
#     def automation_error_message(self):
#         return "Plugin " + self.name + " is not suitable for automation."
# 
# Path: src/plugins/util/file_io.py
# class UnknownFileFormatError(Exception):
# def load_npy(filename, progress_callback=None, segment=None):
# def get_name_after_no_overwrite(name_before, manip, project):
# def save_file(path, data):
# def load_file(filename, progress_callback=None, segment=None):
# def load_reference_frame_npy(filename, offset):
# def load_reference_frame(filename, offset=0):
# 
# Path: src/plugins/util/fileconverter.py
# class RawToNpyConvertError(Exception):
#   def error_msg(self):
# def tif2npy(filename_from, filename_to, progress_callback):
# def raw2npy(filename_from, filename_to, dtype, width, height, num_channels, channel, progress_callback,
#             ignore_shape_error=False):
# 
# Path: src/plugins/util/custom_qt_items.py
# class JSObjectModel(QAbstractTableModel):
# class FileTableModel(JSObjectModel):
# class FileTable(QTableView):
# class ImageStackListView(QListView):
# class MyProgressDialog(QProgressDialog):
# class InfoWidget(QFrame):
# class MyListView(QListView):
# class RoiModel(QStandardItemModel):
# class RoiItemModel(QAbstractListModel):
# class RoiList(QListView):
#     class Labels(object):
#     class Defaults(object):
# class WarningWidget(QFrame):
# class CheckableComboBox(QtGui.QComboBox):
# class MyTableWidget(QTableWidget):
# class PlayerDialog(QDialog):
#   def __init__(self, data, parent=None):
#   def rowCount(self, parent):
#   def columnCount(self, parent): 
#   def data(self, index, role):
#   def headerData(self, section, orientation, role):
#   def retrieve(self, row, key=None):
#   def __init__(self, data, parent=None):
#   def get_path(self, index):
#   def get_entry(self, index):
#   def __init__(self, project=None, parent=None):
#   def selected_paths(self):
#     def __init__(self, parent=None):
#     def contextMenuEvent(self, event):
#   def __init__(self, title, desc, parent=None):
#   def __init__(self, text, parent=None):
#   def setup_ui(self, text):
#   def __init__(self, parent=None):
#   def currentChanged(self, current, previous):
#   def __init__(self, parent=None):
#   def supportedDropActions(self):
#   def dropMimeData(self, data, action, row, column, parent):
#   def flags(self, index):
#   def removeRows(self, row, count, parent):
#   def insertRows(self, row, count, parent):
#     def __init__(self, parent=None):
#     def appendRoi(self, name):
#     def edit_roi_name(self, name, index):
#     def rowCount(self, parent):
#     def data(self, index, role):
#     def setData(self, index, value, role):
#     def flags(self, index):
#     def removeRow(self, roi_to_remove):
#     def __init__(self, widget, roi_types, standard_model=False):
#     def selected_roi_changed(self, selection):
#     def remove_all_rois(self):
#     def setup_params(self, reset=False):
#     def setup_param_signals(self):
#     def prepare_roi_list_for_update(self, selected, deselected):
#     def __init__(self, text, parent=None):
#     def setup_ui(self, text):
#     def __init__(self):
#     def handleItemPressed(self, index):
#   def __init__(self, data=None, *args):
#   def setmydata(self):
#   def update(self, data):
#   def __init__(self, project, filename, parent=None, scaling=True):
#   def show_frame(self, frame_num):
#   def setup_ui(self):
#   def slider_moved(self, value):


# Path: src/plugins/fileimporter.py
import functools
import os
import sys
import traceback
import numpy as np
import psutil
import qtutil
import tifffile as tiff
from shutil import copyfile
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from .util.plugin import PluginDefault
from .util import file_io, fileconverter
from .util import custom_qt_items as cqt


    try:
      fileconverter.tif2npy(filename, path, callback)
    except:
      qtutil.critical('Converting tiff to npy failed.')
      progress.close()
    else:
      ret_filename = path
      with tiff.TiffFile(filename) as tif:
        if rescale_value != 1.00:
          w, h = tif[0].shape
          rescale_width = int(w * rescale_value)
          rescale_height = int(h * rescale_value)
          no_frames = len(tif)
          unscaled = np.load(path)
          try:
            scaled = self.bin_ndarray(unscaled, (no_frames, rescale_height,
                                        rescale_width), callback, operation='mean')
            np.save(path, scaled)
          except:
            qtutil.critical('Rebinning tiff failed. We can only scale down from larger sized files to preserve data')
            progress.close()
    return ret_filename

  def to_npy(self, filename):
    if filename.endswith('.raw'):
      filename = self.convert_raw(filename)
    elif filename.endswith('.tif'):
      filename = self.convert_tif(filename)
    else:

      raise file_io.UnknownFileFormatError()