Merge pull request #220 from ap--/sr2-support

SR2 support

README.md

@@ -90,6 +90,7 @@ To use the pyseabreeze backend (requires `pyusb`) simply run this before importi
 | USB650       |            | ap--/python-seabreeze#47 |
 | SPARK        |     x      |            x             |
 | ADC1000      |            |            x             |
+| SR2          |            |            x             |
 | SR4          |            |            x             |
 | ST-VIS       |            |            x             |
 

os_support/10-oceanoptics.rules

@@ -1,7 +1,7 @@
 # udev rules file for Ocean Optics, Inc. spectrometers
 # ====================================================
 #
-# version: 2.4
+# version: 2.5
 # updated: 2023-04-15
 # maintainer: Andreas Poehlmann <[email protected]>
 #
@@ -14,6 +14,7 @@
 #   $ seabreeze_os_setup
 #
 # Changes:
+# - [2.5] added support for SR2 spectrometer
 # - [2.4] added support for SR4 spectrometer
 # - added support for HDX spectrometer
 # - added support for QE-PRO class of OceanOptics spectrometers
@@ -85,9 +86,11 @@ ATTR{idVendor}=="0547", ATTR{idProduct}=="2235", SYMLINK+="ezUSB-FX-%n", MODE:="
 ATTR{idVendor}=="04b4", ATTR{idProduct}=="8613", SYMLINK+="ezUSB-FX2-%n", MODE:="0666"
 # Ocean Insight Inc. HDX spectrometer
 ATTR{idVendor}=="2457", ATTR{idProduct}=="2003", SYMLINK+="oceanhdx-%n", MODE:="0666"
-# Ocean Insight Inc. SR4 spectrometer
-ATTR{idVendor}=="0999", ATTR{idProduct}=="1002", SYMLINK+="sr4-%n", MODE:="0666"
 # Ocean Insight Inc. ST spectrometer
 ATTR{idVendor}=="0999", ATTR{idProduct}=="1000", SYMLINK+="st-%n", MODE:="0666"
+# Ocean Insight Inc. SR4 spectrometer
+ATTR{idVendor}=="0999", ATTR{idProduct}=="1001", SYMLINK+="sr2-%n", MODE:="0666"
+# Ocean Insight Inc. SR4 spectrometer
+ATTR{idVendor}=="0999", ATTR{idProduct}=="1002", SYMLINK+="sr4-%n", MODE:="0666"
 
 LABEL="oceanoptics_rules_end"

src/seabreeze/pyseabreeze/devices.py

@@ -1202,6 +1202,30 @@ class ADC1000USB(SeaBreezeDevice):
     )
 
 
+class SR2(SeaBreezeDevice):
+    model_name = "SR2"
+
+    # communication config
+    transport = (USBTransport,)
+    usb_vendor_id = 0x0999
+    usb_product_id = 0x1001
+    usb_endpoint_map = EndPointMap(ep_out=0x01, highspeed_in=0x81)
+    usb_protocol = OBP2Protocol
+
+    # spectrometer config
+    dark_pixel_indices = DarkPixelIndices.from_ranges((0, 24))
+    integration_time_min = 1  # 1 us
+    integration_time_max = 2000000  # 2 s
+    integration_time_base = 1
+    spectrum_num_pixel = 2110
+    spectrum_raw_length = (2110 * 2) + 32  # Metadata
+    spectrum_max_value = 65535
+    trigger_modes = TriggerMode.supported("OBP_NORMAL")
+
+    # features
+    feature_classes = (sbf.spectrometer.SeaBreezeSpectrometerFeatureSR2,)
+
+
 class SR4(SeaBreezeDevice):
     model_name = "SR4"
 

src/seabreeze/pyseabreeze/features/spectrometer.py

@@ -604,6 +604,47 @@ def get_intensities(self) -> NDArray[np.float_]:
         return ret * self._normalization_value
 
 
+class SeaBreezeSpectrometerFeatureSR2(SeaBreezeSpectrometerFeatureOBP):
+    def _get_spectrum_raw(self) -> NDArray[np.uint8]:
+        timeout = int(
+            self._integration_time_max * 1e-3
+            + self.protocol.transport.default_timeout_ms
+        )
+        datastring = self.protocol.query(0x000_01C_00, timeout_ms=timeout)
+        return numpy.frombuffer(datastring, dtype=numpy.uint8)
+
+    def get_intensities(self) -> NDArray[np.float_]:
+        tmp = self._get_spectrum_raw()
+        # 32byte metadata block at beginning
+        ret = tmp[32:].view(numpy.dtype("<H")).astype(numpy.double)
+        return ret * self._normalization_value
+
+    def set_trigger_mode(self, mode: int) -> None:
+        if mode in self._trigger_modes:
+            self.protocol.send(0x000_00D_01, mode, request_ack=True)
+        else:
+            raise SeaBreezeError("Only supports: %s" % str(self._trigger_modes))
+
+    def set_integration_time_micros(self, integration_time_micros: int) -> None:
+        t_min = self._integration_time_min
+        t_max = self._integration_time_max
+        if t_min <= integration_time_micros < t_max:
+            i_time = int(integration_time_micros / self._integration_time_base)
+            self.protocol.send(0x000_00C_01, i_time)
+        else:
+            raise SeaBreezeError(f"Integration not in [{t_min:d}, {t_max:d}]")
+
+    def get_wavelengths(self) -> NDArray[np.float_]:
+        data = self.protocol.query(0x000_011_00)
+        num_coeffs = len(data) // 4
+        assert len(data) % 4 == 0  # ???
+        assert num_coeffs > 1  # ???
+        coeffs = struct.unpack("<" + "f" * num_coeffs, data)[1:]
+        # and generate the wavelength array
+        indices = numpy.arange(self._spectrum_length, dtype=numpy.float64)
+        return sum(wl * (indices**i) for i, wl in enumerate(coeffs))  # type: ignore
+
+
 class SeaBreezeSpectrometerFeatureSR4(SeaBreezeSpectrometerFeatureOBP):
     def _get_spectrum_raw(self) -> NDArray[np.uint8]:
         timeout = int(