# Reading Data This section demonstrates how the `isx` package can be used to read data from Inscopix files. Refer to the [file types](../overview) table for reference on the Inscopix file types and read support. :::{note} The following sections assume the `isx` package has been imported, i.e., `import isx` ::: ## Microscope & Behavior Movies `Microscope Movie` and `Behavior Movie` file types can be read using the `isx.Movie` class. ```python # Open the movie for reading movie = isx.Movie.read("movie.isxd") ``` Movie objects have timing and spacing properties which can be accessed: ```python # Timing information can be accessed using: movie.timing # The number of frames can be accessed using: movie.timing.num_samples # The time period can be accessed using: movie.timing.period.secs_float # Spacing information can be accessed using: movie.spacing # The dimensions of the frame can be accessed using: # which will return a 2-tuple containing the dimensions of the frame # (num_rows, num_cols), or (height, width) movie.spacing.num_pixels ``` Frames from movies can be read into memory: ```python # The pixel data type can accessed using: movie.data_type # Read every frame of the movie, and process it for i in range(movie.timing.num_samples): # Dimensions of the frame are (num_rows, num_cols), or (height, width) frame = movie.get_frame_data(i) # Process frame ... ``` ::: {warning} It's recommended to read one frame into memory at a time to prevent out of memory errors. ::: ::: {note} Python indexes by 0, so the first frame is at index 0, and the the second frame is at index 1, and so on. ::: ## Cell Sets `Cell Set` file types can be read using the `isx.CellSet` class. ```python # Open the cell set for reading cell_set = isx.CellSet.read("cell_set.isxd") ``` Similar to movies, cell sets have timing and spacing properties which can be accessed. These properties are derived from the parent movie which generated the cell set. ```python # Timing information can be accessed using: cell_set.timing # The number of frames can be accessed using: cell_set.timing.num_samples # The time period can be accessed using: cell_set.timing.period.secs_float # Spacing information can be accessed using: cell_set.spacing # The dimensions of the frame can be accessed using: # which will return a 2-tuple containing the dimensions of the frame # (num_rows, num_cols), or (height, width) cell_set.spacing.num_pixels ``` Cell data from cell sets can be read into memory: ```python # The number of cells in the cell set can accessed using: cell_set.num_cells # Read data of every cell in the cell set, and process it for i in range(cell_set.num_cells): # Get the cell name name = cell_set.get_cell_name(i) # Get the temporal activity trace of a cell trace = cell_set.get_cell_trace(i) # Get the spatial footprint of a cell footprint = cell_set.get_cell_image_data(i) # Process cell data ... ``` ## Event Sets `Event Set` file types can be read using the `isx.EventSet` class. ```python # open the event set for reading event_set = isx.EventSet.read("event_set.isxd") ``` Similar to cell sets, event sets have timing properties which can be accessed. These properties are derived from the parent cell set which generated the event set. ```python # Timing information can be accessed using: event_set.timing # The number of frames can be accessed using: event_set.timing.num_samples # The time period can be accessed using: event_set.timing.period.secs_float ``` Cell data from event sets can be read into memory: ```python # Read data of every cell in the event set, and process it for i in range(event_set.timing.num_samples): # Get the cell name name = event_set.get_cell_name(i) # Get the event timestamps and amplitudes of a cell offsets, amplitudes = event_set.get_cell_data(i) # Process cell data ... ``` ## Vessel Sets `Vessel Set` file types can be read using the `isx.VesselSet` class. ```python # Open the vessel set for reading vessel_set = isx.VesselSet.read("vessel_set.isxd") ``` Similar to movies, vessel sets have timing and spacing properties which can be accessed. These properties are derived from the parent movie which generated the vessel set. ```python # Timing information can be accessed using: vessel_set.timing # The number of frames can be accessed using: vessel_set.timing.num_samples # The time period can be accessed using: vessel_set.timing.period.secs_float # Spacing information can be accessed using: vessel_set.spacing # The dimensions of the frame can be accessed using: # which will return a 2-tuple containing the dimensions of the frame # (num_rows, num_cols), or (height, width) vessel_set.spacing.num_pixels ``` Vessel data from vessel sets can be read into memory: ```python # The number of vessels in the vessel set can be accessed using: vessel_set.num_vessels # The standard deviation projection image of the parent movie # This is the same for every vessel image = vessel_set.get_vessel_image_data(0) # Read data of every vessel in the vessel set, and process it for i in range(vessel_set.num_vessels): # Get the vessel name name = vessel_set.get_vessel_name(i) # Get the vessel status status = vessel_set.get_vessel_status(i) # For vessel diameter vessel sets, get the following data: # The vessel diameter trace trace = vessel_set.get_vessel_trace_data(i) # The direction of rbc velocity trace center_trace = vessel_set.get_vessel_center_trace_data(i) # The vessel line points line = vessel_set.get_vessel_line_data(i) # For rbc velocity vessel sets, get the following data: # The rbc velocity trace trace = vessel_set.get_vessel_trace_data(i) # The direction of rbc velocity trace direction_trace = vessel_set.get_vessel_direction_trace_data(i) # The first correlation heatmap of the vessel corr = vessel_set.get_vessel_correlations_data(i, 0) # The vessel box points box = vessel_set.get_vessel_line_data(i) # Process vessel data ... ``` ## GPIO & IMU `GPIO` and `IMU` file types can be read using the `isx.GpioSet` class. ```python # open the gpio set for reading gpio_set = isx.GpioSet.read("signals.gpio") ``` Gpio sets have timing properties which can be accessed. ```python # Timing information can be accessed using: gpio_set.timing # The number of frames can be accessed using: gpio_set.timing.num_samples # The time period can be accessed using: gpio_set.timing.period.secs_float ``` Signal data from gpio sets can be read into memory: ```python # Number of channels (i.e., signals) can be accessed using: gpio_set.num_channels # Read data of every cell in the cell set, and process it for i in range(gpio_set.num_channels): # Get the channel name name = gpio_set.get_channel_name(i) # Get the signal timestamps and amplitudes of a channel offsets, amplitudes = gpio_set.get_channel_data(i) # Process signal data ... ```