polyTEM.utilities.read_mdoc

polyTEM.utilities.read_mdoc(filename: str)

Reads the mdoc file generated during imaging and extracts parameters

Expected file contents: T = SerialEM: Glacios 9953405 at Stanford University 26-Oct-23 14:55:45 Voltage = 200

[FrameSet = 0] GainReference = CountRef_AM880_2_area_2_0000_0.0.mrc TiltAngle = 0.00440576 StagePosition = -26.4387 53.0248 StageZ = -71.9289 Magnification = 36000 Intensity = 0.456253 ExposureDose = 0 DoseRate = 12.9769 PixelSpacing = 1.151 SpotSize = 5 ProbeMode = 0 Defocus = 0.166593 ImageShift = 0 0 RotationAngle = -92.83 ExposureTime = 3.59521 Binning = 1 CameraIndex = 1 DividedBy2 = 0 OperatingMode = 1 UsingCDS = 0 MagIndex = 31 LowDoseConSet = 4 CountsPerElectron = 1 TargetDefocus = -1 SubFramePath = 192.168.42.2dataSalleoChristina‚31026_AM880AM880_2_-1um_area_11_0000.mrc NumSubFrames = 18 FrameDosesAndNumber = 0 18 DateTime = 26-Oct-2023 17:06:51 NavigatorLabel = 11 UncroppedSize = -5760 -4092 RotationAndFlip = 0 TimeStamp = 120499611

Parameters:

filename – .mrc.mdoc filename

Returns:

float, angstroms per pixel defocus: float, target defocus

Return type:

pixel_res