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feat(utils/opatio): updated save to ascii function and fixed minor bug in loader

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the new general purpose index design introduced a bug in the loader related to the byte position of the byteStart field. This has been resolved. Further, I have updated the save to ascii format to provide an explicit warning that the ascii version is only for debugging purposes and not meant to be used directly.
This commit is contained in:
Emily Boudreaux
2025-02-16 20:44:45 -05:00
parent 4ac9340804
commit 131161e1bd
1 changed files with 26 additions and 21 deletions
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47
utils/opatio/src/opatio/opat/opat.py
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@@ -249,7 +249,7 @@ class OpatIO:
logKappa = logKappa
)
self.tables.append(indicies, table))
self.tables.append((indicies, table))
self.header.numTables += 1
@@ -309,7 +309,7 @@ class OpatIO:
)
tableIndexBytes += tableIndex.sha256
if len(tableIndexBytes) != 64:
if len(tableIndexBytes) != 16+self.header.numIndex*8+32:
raise RuntimeError(f"Each table index entry must have 64 bytes. Due to an unknown error the table index entry for (X,Z)=({tableIndex.X},{tableIndex.Z}) header has {len(tableIndexBytes)} bytes")
return tableIndexBytes
@@ -347,7 +347,8 @@ class OpatIO:
tableString.append(" ".join(tableIndexString))
tableString.append("-" * 80)
# write logR across the top (reserving one col for where logT will be)
logRRow = f"{'':<10}"
tableString.append(f"{'':<10}{'logR':<10}")
logRRow = f"{'logT':<10}"
logRRowTrue = "".join(f"{r:<10.4f}" for r in table.logR)
tableString.append(logRRow + logRRowTrue)
for i, logT in enumerate(table.logT):
@@ -411,21 +412,27 @@ class OpatIO:
currentStartByte += len(tableBytes)
self.header.indexOffset = currentStartByte
with open(filename, 'w') as f:
f.write(f"{self.header.magic}\n")
f.write(f"Version: {self.header.version}\n")
f.write(f"numTables: {self.header.numTables}\n")
f.write(f"headerSize (bytes): {self.header.headerSize}\n")
f.write(f"tableIndex Offset (bytes): {self.header.indexOffset}\n")
f.write(f"Creation Date: {self.header.creationDate}\n")
f.write(f"Source Info: {self.header.sourceInfo}\n")
f.write(f"Comment: {self.header.comment}\n")
f.write(f"numIndex: {self.header.numIndex}\n")
f.write("="*80 + "\n")
f.write("This is an ASCII representation of an OPAT file, it is not a valid OPAT file in and of itself.\n")
f.write("This file is meant to be human readable and is not meant to be read by a computer.\n")
f.write("The purpose of this file is to provide a human readable representation of the OPAT file which can be used for debugging purposes.\n")
f.write("The full binary specification of the OPAT file can be found in the OPAT file format documentation at:\n")
f.write(" https://github.com/4D-STAR/4DSSE/blob/main/specs/OPAT/OPAT.pdf\n")
f.write("="*35 + " HEADER " + "="*36 + "\n")
f.write(f">> {self.header.magic}\n")
f.write(f">> Version: {self.header.version}\n")
f.write(f">> numTables: {self.header.numTables}\n")
f.write(f">> headerSize (bytes): {self.header.headerSize}\n")
f.write(f">> tableIndex Offset (bytes): {self.header.indexOffset}\n")
f.write(f">> Creation Date: {self.header.creationDate}\n")
f.write(f">> Source Info: {self.header.sourceInfo}\n")
f.write(f">> Comment: {self.header.comment}\n")
f.write(f">> numIndex: {self.header.numIndex}\n")
f.write("="*37 + " DATA " + "="*37 + "\n")
f.write("="*80 + "\n")
for tableString in tableStrings:
f.write(tableString)
f.write("="*80 + "\n")
f.write("="*80 + "\n")
f.write("="*36 + " INDEX " + "="*37 + "\n")
f.write(self.print_table_indexes(tableIndexs))
def save(self, filename: str) -> str:
@@ -501,13 +508,11 @@ def loadOpat(filename: str) -> OpatIO:
while tableIndexEntryBytes := f.read(tableIndexChunkSize):
unpackedTableIndexEntry = struct.unpack(tableIndexFMTString, tableIndexEntryBytes)
checksum = f.read(32)
# TODO: Update this to get the fully, general header index set (currently it still gets only X and Z without the update)
# TODO: Also update the spec to reflect the new header index set and the new table index format.
index = unpackedTableIndexEntry[:loadedHeader.numIndex]
tableIndexEntry = TableIndex(
X = unpackedTableIndexEntry[0],
Z = unpackedTableIndexEntry[1],
byteStart = unpackedTableIndexEntry[2],
byteEnd = unpackedTableIndexEntry[3],
index = index,
byteStart = unpackedTableIndexEntry[loadedHeader.numIndex],
byteEnd = unpackedTableIndexEntry[loadedHeader.numIndex+1],
sha256 = checksum
)
tableIndices.append(tableIndexEntry)
@@ -530,5 +535,5 @@ def loadOpat(filename: str) -> OpatIO:
logT = np.array(unpackedData[N_R: N_R+N_T], dtype=np.float64)
logKappa = np.array(unpackedData[N_R+N_T:], dtype=np.float64).reshape((N_R, N_T))
opat.add_table(tableIndex.X, tableIndex.Z, logR, logT, logKappa)
opat.add_table(tableIndex.index, logR, logT, logKappa)
return opat