pyadps 0.1.0b0__py3-none-any.whl → 0.1.1__py3-none-any.whl

pyadps/utils/pyreadrdi.py

@@ -320,7 +320,7 @@ def safe_read(bfile, num_bytes):
 
         if len(readbytes) != num_bytes:
             print(f"Unexpected end of file: fewer than {num_bytes} bytes were read.")
-            return (readbytes, ErrorCode.FILE_CORRUPTED)
+            return (None, ErrorCode.FILE_CORRUPTED)
         else:
             return (readbytes, ErrorCode.SUCCESS)
 
@@ -427,6 +427,7 @@ def fileheader(rdi_file):
                 error = ErrorCode.WRONG_RDIFILE_TYPE
                 print(bcolors.FAIL + error.message + bcolors.ENDC)
                 error_code = error.code
+                dummytuple = ([], [], [], [], [], ensemble, error_code)
                 return dummytuple
         else:
             if headerid[i] != 127 or sourceid[i] != 127:
@@ -442,8 +443,14 @@ def fileheader(rdi_file):
                 print(f"Ensembles reset to {i}" + bcolors.ENDC)
                 break
 
-        data = unpack("H" * datatype[i], dbyte)
-        address_offset.append(data)
+        try:
+            data = unpack("H" * datatype[i], dbyte)
+            address_offset.append(data)
+        except:
+            error = ErrorCode.FILE_CORRUPTED
+            error_code = error.code
+            dummytuple = ([], [], [], [], [], ensemble, error_code)
+            return dummytuple
 
         skip_array = [None] * datatype[i]
         for dtype in range(datatype[i]):
@@ -553,7 +560,7 @@ def fixedleader(rdi_file, byteskip=None, offset=None, idarray=None, ensemble=0):
         fbyteskip = None
         for count, item in enumerate(idarray[i]):
             if item in (0, 1):
-                fbyteskip = offset[1][count]
+                fbyteskip = offset[0][count]
         if fbyteskip == None:
             error = ErrorCode.ID_NOT_FOUND
             ensemble = i
@@ -703,7 +710,7 @@ def variableleader(rdi_file, byteskip=None, offset=None, idarray=None, ensemble=
         fbyteskip = None
         for count, item in enumerate(idarray[i]):
             if item in (128, 129):
-                fbyteskip = offset[1][count]
+                fbyteskip = offset[0][count]
         if fbyteskip == None:
             error = ErrorCode.ID_NOT_FOUND
             ensemble = i
@@ -883,7 +890,7 @@ def datatype(
 
     # These arguments are outputs of fixedleader function.
     # Makes the code faster if the fixedheader function is already executed.
-    if cell == 0 or beam == 0:
+    if isinstance(cell, (np.integer, int)) or isinstance(beam, (np.integer, int)):
         flead, ensemble, fl_error_code = fixedleader(
             filename,
             byteskip=byteskip,
@@ -891,22 +898,23 @@ def datatype(
             idarray=idarray,
             ensemble=ensemble,
         )
-        cell = int(flead[7][0])
-        beam = int(flead[6][0])
+        cell = []
+        beam = []
+        cell = flead[7][:]
+        beam = flead[6][:]
         if fl_error_code != 0:
             error_code = fl_error_code
     else:
-        cell = int(cell)
-        beam = int(beam)
-
+        cell = cell
+        beam = beam
     # Velocity is 16 bits and all others are 8 bits.
     # Create empty array for the chosen variable name.
     if var_name == "velocity":
-        var_array = np.zeros((beam, cell, ensemble), dtype="int16")
+        var_array = np.full((int(max(beam)), int(max(cell)), ensemble), -32768, dtype="int16")
         bitstr = "<h"
         bitint = 2
     else:  # inserted
-        var_array = np.zeros((beam, cell, ensemble), dtype="uint8")
+        var_array = np.zeros((int(max(beam)), int(max(cell)), ensemble), dtype="uint8")
         bitstr = "<B"
         bitint = 1
     # -----------------------------
@@ -935,7 +943,9 @@ def datatype(
     fbyteskip = None
     for count, item in enumerate(idarray[0][:]):
         if item in vid:
-            fbyteskip = offset[1][count]
+            fbyteskip = []
+            for i in range(ensemble):
+                fbyteskip.append(int(offset[i][count]))
             break
     if fbyteskip is None:
         print(
@@ -948,10 +958,10 @@ def datatype(
 
     # READ DATA
     for i in range(ensemble):
-        bfile.seek(fbyteskip, 1)
+        bfile.seek(fbyteskip[i], 1)
         bdata = bfile.read(2)
-        for cno in range(cell):
-            for bno in range(beam):
+        for cno in range(int(cell[i])):
+            for bno in range(int(beam[i])):
                 bdata = bfile.read(bitint)
                 varunpack = unpack(bitstr, bdata)
                 var_array[bno][cno][i] = varunpack[0]

pyadps/utils/readrdi.py

@@ -3,9 +3,9 @@
 """
 RDI ADCP Binary File Reader
 ===========================
-This module provides classes and functions to read and extract data from RDI Acoustic Doppler 
-Current Profiler (ADCP) binary files. The module supports Workhorse, Ocean Surveyor, and DVS ADCPs. 
-It allows for parsing of various data types such as Fixed Leader, Variable Leader, Velocity, Correlation, 
+This module provides classes and functions to read and extract data from RDI Acoustic Doppler
+Current Profiler (ADCP) binary files. The module supports Workhorse, Ocean Surveyor, and DVS ADCPs.
+It allows for parsing of various data types such as Fixed Leader, Variable Leader, Velocity, Correlation,
 Echo Intensity, Percent Good, and Status data.
 
 Classes
@@ -28,7 +28,7 @@ Status
     Parses the status data from the ADCP.
 ReadFile
     Manages the entire data extraction process and unifies all data types.
-    
+
 Functions
 ---------
 check_equal(array)
@@ -101,6 +101,7 @@ import os
 import sys
 
 import numpy as np
+import pandas as pd
 from pyadps.utils import pyreadrdi
 
 
@@ -129,9 +130,7 @@ class DotDict:
             #     with open(json_file_path, "r") as file:
             #         dictionary = json.load(file)
             else:
-                dictionary = (
-                    {}
-                )  # Initialize an empty dictionary if no JSON file is found
+                dictionary = {}  # Initialize an empty dictionary if no JSON file is found
         self._initialize_from_dict(dictionary)
 
     def _initialize_from_dict(self, dictionary):
@@ -326,7 +325,7 @@ class FileHeader:
         """
         file_stats = os.stat(self.filename)
         sys_file_size = file_stats.st_size
-        cal_file_size = sum(self.bytes) + 2 * len(self.bytes)
+        cal_file_size = sum((self.bytes).astype(int)) + 2 * len(self.bytes)
 
         check = dict()
 
@@ -435,7 +434,7 @@ def flead_dict(fid, dim=2):
         "False Target Thresh": "int64",
         "Spare 1": "int64",
         "Transmit Lag Dist": "int64",
-        "CPU Serial No": "int64",
+        "CPU Serial No": "int128",
         "System Bandwidth": "int64",
         "System Power": "int64",
         "Spare 2": "int64",
@@ -447,9 +446,15 @@ def flead_dict(fid, dim=2):
     counter = 1
     for key, value in fname.items():
         if dim == 2:
-            flead[key] = getattr(np, value)(fid[:][counter])
+            if key == "CPU Serial No":
+                flead[key] = np.uint64(fid[:][counter])
+            else:
+                flead[key] = np.int64(fid[:][counter])
         elif dim == 1:
-            flead[key] = getattr(np, value)(fid[counter])
+            if key == "CPU Serial No":
+                flead[key] = np.uint64(fid[counter])
+            else:
+                flead[key] = np.int64(fid[counter])
         else:
             print("ERROR: Higher dimensions not allowed")
             sys.exit()
@@ -505,6 +510,7 @@ class FixedLeader:
         )
         self.warning = pyreadrdi.ErrorCode.get_message(self.error)
 
+        self.data = np.uint64(self.data)
         self.fleader = flead_dict(self.data)
         self._initialize_from_dict(DotDict(json_file_path="flmeta.json"))
 
@@ -800,7 +806,8 @@ def vlead_dict(vid):
 
     counter = 1
     for key, value in vname.items():
-        vlead[key] = getattr(np, value)(vid[:][counter])
+        # vlead[key] = getattr(np, value)(vid[:][counter])
+        vlead[key] = vid[:][counter]
         counter += 1
 
     return vlead
@@ -877,7 +884,7 @@ class VariableLeader:
             setattr(getattr(self, key), "data", self.data[i])
             i = i + 1
 
-    def bit_result(self):
+    def bitresult(self):
         """
         Extracts Bit Results from Variable Leader (Byte 13 & 14)
         This field is part of the WorkHorse ADCP’s Built-in Test function.
@@ -956,8 +963,6 @@ class VariableLeader:
 
         scale_factor = scale_list.get(fixclass["Frequency"])
 
-        print(fixclass["Frequency"])
-
         channel["Xmit Voltage"] = adc1 * (scale_factor[0] / 1000000)
 
         channel["Xmit Current"] = adc0 * (scale_factor[1] / 1000000)
@@ -974,6 +979,80 @@ class VariableLeader:
 
         return channel
 
+    def error_status_word(self, esw=1):
+        bitset1 = (
+            "Bus Error exception",
+            "Address Error exception",
+            "Zero Divide exception",
+            "Emulator exception",
+            "Unassigned exception",
+            "Watchdog restart occurred",
+            "Batter Saver Power",
+        )
+
+        bitset2 = (
+            "Pinging",
+            "Not Used 1",
+            "Not Used 2",
+            "Not Used 3",
+            "Not Used 4",
+            "Not Used 5",
+            "Cold Wakeup occured",
+            "Unknown Wakeup occured",
+        )
+
+        bitset3 = (
+            "Clock Read error occured",
+            "Unexpected alarm",
+            "Clock jump forward",
+            "Clock jump backward",
+            "Not Used 6",
+            "Not Used 7",
+            "Not Used 8",
+            "Not Used 9",
+        )
+
+        bitset4 = (
+            "Not Used 10",
+            "Not Used 11",
+            "Not Used 12",
+            "Power Fail Unrecorded",
+            "Spurious level 4 intr DSP",
+            "Spurious level 5 intr UART",
+            "Spurious level 6 intr CLOCK",
+            "Level 7 interrup occured",
+        )
+
+        if esw == 1:
+            bitset = bitset1
+            errorarray = self.vleader["Error Status Word 1"]
+        elif esw == 2:
+            bitset = bitset2
+            errorarray = self.vleader["Error Status Word 2"]
+        elif esw == 3:
+            bitset = bitset3
+            errorarray = self.vleader["Error Status Word 3"]
+        else:
+            bitset = bitset4
+            errorarray = self.vleader["Error Status Word 4"]
+
+        errorstatus = dict()
+        # bitarray = np.zeros(32, dtype='str')
+
+        for item in bitset:
+            errorstatus[item] = np.array([])
+
+        for data in errorarray:
+            byte_split = format(data, "08b")
+            bitposition = 0
+            for item in bitset:
+                errorstatus[item] = np.append(
+                    errorstatus[item], byte_split[bitposition]
+                )
+                bitposition += 1
+
+        return errorstatus
+
 
 class Velocity:
     """
@@ -1027,7 +1106,7 @@ class Velocity:
         self.cells = cell
         self.beams = beam
 
-        self.units = "mm/s"
+        self.unit = "mm/s"
         self.missing_value = "-32768"
         self.scale_factor = 1
         self.valid_min = -32768
@@ -1086,7 +1165,7 @@ class Correlation:
         self.cells = cell
         self.beams = beam
 
-        self.units = ""
+        self.unit = ""
         self.scale_factor = 1
         self.valid_min = 0
         self.valid_max = 255
@@ -1145,7 +1224,7 @@ class Echo:
         self.cells = cell
         self.beams = beam
 
-        self.units = "counts"
+        self.unit = "counts"
         self.scale_factor = "0.45"
         self.valid_min = 0
         self.valid_max = 255
@@ -1204,7 +1283,7 @@ class PercentGood:
         self.cells = cell
         self.beams = beam
 
-        self.units = "percent"
+        self.unit = "percent"
         self.valid_min = 0
         self.valid_max = 100
         self.long_name = "Percent Good"
@@ -1262,7 +1341,7 @@ class Status:
         self.cells = cell
         self.beams = beam
 
-        self.units = ""
+        self.unit = ""
         self.valid_min = 0
         self.valid_max = 1
         self.long_name = "Status Data Format"
@@ -1390,6 +1469,47 @@ class ReadFile:
             warning_array["Status"] = self.status.warning
             ensemble_array["Status"] = self.status.ensembles
 
+        # Add Time Axis
+        year = self.variableleader.vleader["RTC Year"]
+        month = self.variableleader.vleader["RTC Month"]
+        day = self.variableleader.vleader["RTC Day"]
+        hour = self.variableleader.vleader["RTC Hour"]
+        minute = self.variableleader.vleader["RTC Minute"]
+        second = self.variableleader.vleader["RTC Second"]
+        year = year + 2000
+        date_df = pd.DataFrame(
+            {
+                "year": year,
+                "month": month,
+                "day": day,
+                "hour": hour,
+                "minute": minute,
+                "second": second,
+            }
+        )
+        self.time = pd.to_datetime(date_df)
+
+        # Depth
+        # Create a depth axis with mean depth in 'm'
+        cell1 = self.fixedleader.field()["Cells"]
+        bin1dist1 = self.fixedleader.field()["Bin 1 Dist"] / 100
+        depth_cell_len1 = self.fixedleader.field()["Depth Cell Len"] / 100
+        beam_direction1 = self.fixedleader.system_configuration()["Beam Direction"]
+        mean_depth = np.mean(self.variableleader.vleader["Depth of Transducer"]) / 10
+        mean_depth = np.trunc(mean_depth)
+        if beam_direction1.lower() == "up":
+            sgn = -1
+        else:
+            sgn = 1
+        first_depth = mean_depth + sgn * bin1dist1
+        last_depth = first_depth + sgn * cell1 * depth_cell_len1
+        z = np.arange(first_depth, last_depth, sgn * depth_cell_len1)
+        self.depth = z
+
+        # Add all attributes/method/data from FixedLeader and VariableLeader
+        self._copy_attributes_from_var()
+
+        # Error Codes and Warnings
         self.error_codes = error_array
         self.warnings = warning_array
         self.ensemble_array = ensemble_array
@@ -1405,6 +1525,33 @@ class ReadFile:
         else:
             self.isWarning = True
 
+        # Add additional attributes
+        # Ensemble
+        dtens = self.ensemble_value_array
+        minens = np.min(dtens)
+        self.ensembles = minens
+
+        # Add attribute that lists all variables/functions
+        self.list_vars = list(vars(self).keys())
+
+    def _copy_attributes_from_var(self):
+        for attr_name, attr_value in self.variableleader.__dict__.items():
+            # Copy each attribute of var into self
+            setattr(self, attr_name, attr_value)
+        for attr_name, attr_value in self.fixedleader.__dict__.items():
+            # Copy each attribute of var into self
+            setattr(self, attr_name, attr_value)
+
+    def __getattr__(self, name):
+        # Delegate attribute/method access to self.var if not found in self
+        if hasattr(self.variableleader, name):
+            return getattr(self.variableleader, name)
+        if hasattr(self.fixedleader, name):
+            return getattr(self.fixedleader, name)
+        raise AttributeError(
+            f"'{self.__class__.__name__}' object has no attribute '{name}'"
+        )
+
     def fixensemble(self, min_cutoff=0):
         """
         Fixes the ensemble size across all data types in the file if they differ.